A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
Home Page: https://www.cog-genomics.org/plink/2.0/
There seems to be new functionality (since 1.90b2k) that compiles Rconnections.cc which appears to require a config.h file (I presume this is of the type generated by autoconf's ./configure). However, the source tree doesn't include any autoconf files.
How are we meant to generate an appropriate config.h?
Starting from a multifamily joint-called VCF, I'm trying to use the '--mendel' option to detect mendelian errors based on pedigree information I supplied. But by comparison to another method, it appears to be missing many such errors when there is a multi-allelic (more than one alt) variant with mend errors in multiple families on multiple variants. I have boiled down an example in the attached zip file - a one variant VCF containing seven people over two families. Each of the affecteds should be a mendelian error, but only the ones in the first family (601) get detected, the mendelian error in family 643 is not reported.
But if you edit the VCF and change the two HET calls for the 601 children (0/2 --> 0/0), and repeat, then the error in family 643 IS reported.
Thanks
Hello!
I'd like to use PLINK 1.9 (Linux 64-bit) on my Windows 10 PC, using the fairly new WSL Ubuntu (https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux).
Unfortunately, when I try using it, I get a segmentation fault. Are any of you able to run PLINK 1.9 on Windows, or is there a general incompatibility btwn. WSL and PLINK 1.9 at the moment?
Best
Michael
bcftools -Ob and --bcf option, I found out all haploid calls on chr23 (chrX: Non-PAR) region are ignored (ex.1).bcftools -Oz and --vcf option, these calls are handled properly (ex.2).bcf_to_bed function, but not sure whether the issue is due to plink or bcftools, so I decided to just post this.% bcftools -v
bcftools 1.1-141-g10cb60e
Using htslib 1.1-125-g3768707
Copyright (C) 2014 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
% plink --version
PLINK v1.90b3b 64-bit (15 Jan 2015)
bcftools -Ob and --bcf]Here's a quick example with 1KGP phase3_v5 dataset to replicate the issue (need to update .fam file for using --fileter-males)
% bcftools view -Ob -r X:2699555 ALL.chrX.phase3_shapeit2_mvncall_integrated.20130502.genotypes.vcf.gz | plink --bcf /dev/stdin --out test
PLINK v1.90b3b 64-bit (15 Jan 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to test.log.
96695 MB RAM detected; reserving 48347 MB for main workspace.
--bcf: test.bed + test.bim + test.fam written.
# need to update the sex column
% plink --bfile test --filter-males --missing --out test
PLINK v1.90b3b 64-bit (15 Jan 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to test.log.
96695 MB RAM detected; reserving 48347 MB for main workspace.
1 variant loaded from .bim file.
2504 people (1233 males, 1271 females) loaded from .fam.
1271 people removed due to gender filter (--filter-males).
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1229 founders and 4 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate in remaining samples is 0.
--missing: Sample missing data report written to test.imiss, and variant-based
missing data report written to test.lmiss.
% cat test.lmiss
CHR SNP N_MISS N_GENO F_MISS
23 rs311165 1233 1233 1
bcftools -Oz and --vcf]% bcftools view -Oz -r X:2699555 ALL.chrX.phase3_shapeit2_mvncall_integrated.20130502.genotypes.vcf.gz | plink --vcf /dev/stdin --out test2
PLINK v1.90b3b 64-bit (15 Jan 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to test2.log.
96695 MB RAM detected; reserving 48347 MB for main workspace.
--vcf: test2.bed + test2.bim + test2.fam written.
# update fam
% plink --bfile test2 --filter-males --missing --out test2
PLINK v1.90b3b 64-bit (15 Jan 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to test2.log.
96695 MB RAM detected; reserving 48347 MB for main workspace.
1 variant loaded from .bim file.
2504 people (1233 males, 1271 females) loaded from .fam.
1271 people removed due to gender filter (--filter-males).
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1229 founders and 4 nonfounders present.
Calculating allele frequencies... done.
--missing: Sample missing data report written to test2.imiss, and variant-based
missing data report written to test2.lmiss.
% cat test2.lmiss
CHR SNP N_MISS N_GENO F_MISS
23 rs311165 0 1233 0
Hi! I the newest version for unix (non avx) seems to have issues opening bgen 1.2 files (from UKBB). Detailed command line below. Thanks for working on this tool! Markus
running PLINK v2.00a2LM 64-bit Intel (15 Feb 2018) with bgen 1.2 input files gives "Error: File read failure."
command:
plink2 --bgen ukb_imp_chr22_v2.bgen --sample ukb672_imp_chr22_v2_s487406.sample --make-pgen --out testchr22
Running the same as above using PLINK v2.00a1LM 64-bit Intel (24 Jan 2018) works.
Currently, the --R option allows to connect to a local TCP service in a port specified by --R-port or the default one. However, when running the Plink-Rserve combination on shared systems such as cluster computing nodes, Rserve regularly fails as the default port is already taken by some other process, be it Rserve or not. Therefore, Rserve also allows to use a unix domain socket instead, where no clash will happen with other users.
Technically, in Rconnection.cc, connecting to those sockets is already implemented. If the port is negative, the given IP string is intepreted as a path to a unix domain socket and the family correctly set to AF_LOCAL instead if AF_INET. Unfortunately, the option parser in plink.c for --R-port expects a positive number and an IP (or host name) cannot be given at all.
It would be nice if someone could add the additional option, e.g. --R-host, and lift the positive-integer restriction on the --R-port option. As a side effect, that would also allow connecting to remote Rserve instances.
hello,
My shell is
plink --vcf GWAS.23chr.vcf \
--a2-allele GWAS.23chr.vcf.ref \
--keep-allele-order \
--double-id \
--set-missing-var-ids @:# \
--allow-no-sex \
--update-sex pheno.gender.txt 3 \
--pheno pheno.gender.txt --mpheno 4 \
--recode \
--make-bed \
--out vcf2plink && \
plink --file vcf2plink --maf 0.05 --geno 0.1 --hwe 0.000005 --mind 0.2 --make-bed --recode --out plink.filter &&\
plink --bfile plink.filter --assoc --out plink_asso --allow-no-sex
The pheno.gender.txt file contains gender information, how dose PLINK consider male and female samples for chromosome X results?
thank you
best
Hi, thanks for putting so much work into a fantastic piece of software. I've been working on using plink style binary files in one of my own programs and have come across an inconsistency in the documentation that I think could use some clarification.
On the original plink1.07 webpage, the .bed format is given to have the following conversions:
For the genotype data, each byte encodes up to four genotypes (2 bits per genoytpe). The coding is
00 Homozygote "1"/"1"
01 Heterozygote
11 Homozygote "2"/"2"
10 Missing genotype
While on the plink1.9 webpage, the conversion table is given as follows:
The two-bit genotype codes have the following meanings:
00 Homozygous for first allele in .bim file
01 Missing genotype
10 Heterozygous
11 Homozygous for second allele in .bim file
There seems to be some disagreement between the heterozygous and missing codings.
I downloaded the toy data distributed with plink1.9 and converted it to binary.
plink2 --bfile toy --make-bed --out toy
cat toy.ped
1 1000000000 0 0 1 1 0 0 1 1
1 1000000001 0 0 1 2 1 1 1 2
xxd -b toy.bed
0000000: 01101100 00011011 00000001 00001101 00001011 l....
cat toy.bim
1 rs0 0 1000 0 1
1 rs10 0 1001 2 1
After excluding the first two magic number bytes and the format byte, we proceed to look at the first (fourth) byte which reads
rs0
10 - missing (1.07) / heterozygous (?) (1.9)
11 - homozygous second allele
...skip...
rs10
11 - homozygous second allele
01 - heterozygote (1.07) / missing (?) (1.9)
...skip...
So, it seems as though this simple example supports the original v1.07 coding, unless I have misinterpreted it.
plink1.07 and plink1.9 for missing / heterozygous? If so, is there any way to distinguish the two and account for that?hi
I run plink v1.07 Association mapping with segmental CNV data: regional tests
the EMP1 and EMP2 of every region is 1
my vcf is
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CP1600001 CP1600002 CP1600003 CP1600004 CP1600005 CP1600006 CP1600007 CP1600008 CP1600009 CP1600010 CP1600011 CP1600012 CP1600013 CP1600014 CP1600015 CP1600016 CP1600017 CP1600018 CP1600019 CP1600020 CP1600021 CP1600022 CP1600023 CP1600024 CP1600025 CP1600026 CP1600027 CP1600028 CP1600029 CP1600030 CP1600031 CP1600032 CP1600033 CP1600034 CP1600035 CP1600036 CP1600037 CP1600038 CP1600039 CP1600040 CP1600041
1 790997 CNV_1_790997_830957 T <CN0>,<CN2> . PASS END=830957;GCFRACTION=0.43;GCLENGTH=39961;GLALTFREQ=NA;GLALTSUM=0.000;GLHETSUM=0.000;GLINBREEDINGCOEFF=NA;GLREFFREQ=NA;GLREFSUM=0.000;GSCALLRATE=0.999;GSCLUSTERSEP=9.59;GSCLUSTERSEPWEIGHTEDMEAN=8.03;GSCLUSTERSEPWEIGHTEDMEDIAN=8.14;GSCNALLELES=3;GSCNCATEGORY=MIXED;GSCNDIST=0,3,794,152,18;GSCNMAX=4;GSCNMIN=1;GSCNQUAL=2181.9075;GSDUPLICATEOVERLAP=NA;GSDUPLICATES=NA;GSDUPLICATESCORE=NA;GSELENGTH=26499;GSEXPMEAN=189.3918;GSGMMWEIGHTS=0.0001,0.0031,0.8205,0.1577,0.0186,0.0000;GSM1=1.0647;GSM2=0.3106,1.5530;GSNNONREF=173;GSNONVARSCORE=NA;GSNVARIANT=173;SVTYPE=CNV GT:CN:CNF:CNL:CNP:CNQ:GL:GP:GQ 0/2:3:2.9985:-1000.00,-110.41,-13.72,-0.00,-7.01,-22.31:-1000.00,-112.12,-13.01,-0.00,-7.94,-59.86:79.4:-14.20,-110.41,-1000.00,-0.00,-13.90,-7.01:-12.47,-113.83,-1000.00,-0.00,-15.91,-8.95:79 0/0:2:2.2905:-1000.00,-46.59,-0.00,-3.71,-19.97,-41.26:-1000.00,-49.01,-0.00,-4.42,-21.62,-79.53:44.2:-0.48,-46.59,-1000.00,-3.71,-0.18,-19.97:-0.00,-51.26,-1000.00,-4.96,-3.44,-23.17:34 0/0:2:2.0602:-1000.00,-31.48,-0.00,-8.33,-26.61,-48.86:-1000.00,-33.90,-0.00,-9.05,-28.26,-87.12:90.5:-0.48,-31.48,-1000.00,-8.33,-0.18,-26.61:-0.00,-36.15,-1000.00,-9.59,-3.44,-29.81:34 0/0:2:2.0828:-1000.00,-34.69,-0.00,-8.34,-27.44,-50.83:-1000.00,-37.12,-0.00,-9.06,-29.08,-89.09:90.6:-0.48,-34.69,-1000.00,-8.34,-0.18,-27.44:-0.00,-39.37,-1000.00,-9.60,-3.44,-30.63:34 0/0:2:2.0486:-1000.00,-32.82,-0.00,-9.11,-28.69,-52.45:-1000.00,-35.24,-0.00,-9.82,-30.33,-90.71:98.2:-0.48,-32.82,-1000.00,-9.11,-0.18,-28.69:-0.00,-37.49,-1000.00,-10.36,-3.44,-31.88:34 0/2:3:2.9220:-1000.00,-106.42,-12.13,-0.00,-8.40,-25.00:-1000.00,-108.13,-11.42,-0.00,-9.32,-62.55:93.2:-12.61,-106.42,-1000.00,-0.00,-12.31,-8.40:-10.88,-109.84,-1000.00,-0.00,-14.32,-10.33:93 0/0:2:2.0621:-1000.00,-32.94,-0.00,-8.65,-27.68,-50.87:-1000.00,-35.36,-0.00,-9.36,-29.33,-89.13:93.6:-0.48,-32.94,-1000.00,-8.65,-0.18,-27.68:-0.00,-37.61,-1000.00,-9.90,-3.44,-30.88:34 0/0:2:1.9514:-1000.00,-25.78,-0.00,-10.57,-30.21,-53.49:-1000.00,-28.20,-0.00,-11.28,-31.86,-91.75:99.0:-0.48,-25.78,-1000.00,-10.57,-0.18,-30.21:-0.00,-30.45,-1000.00,-11.82,-3.44,-33.41:34 0/0:2:2.1869:-1000.00,-36.41,-0.00,-5.42,-21.29,-41.33:-1000.00,-38.83,-0.00,-6.14,-22.93,-79.59:61.4:-0.48,-36.41,-1000.00,-5.42,-0.18,-21.29:-0.00,-41.08,-1000.00,-6.68,-3.44,-24.48:34 0/0:2:2.0285:-1000.00,-30.43,-0.00,-9.17,-28.24,-51.25:-1000.00,-32.85,-0.00,-9.89,-29.88,-89.51:98.9:-0.48,-30.43,-1000.00,-9.17,-0.18,-28.24:-0.00,-35.10,-1000.00,-10.43,-3.44,-31.43:34 0/2:3:2.7910:-1000.00,-88.50,-8.20,-0.00,-9.81,-26.83:-1000.00,-90.21,-7.48,-0.00,-10.74,-64.37:74.8:-8.68,-88.50,-1000.00,-0.00,-8.38,-9.81:-6.94,-91.92,-1000.00,-0.00,-10.38,-11.75:69 0/0:2:1.9336:-1000.00,-24.42,-0.00,-10.74,-30.25,-53.28:-1000.00,-26.84,-0.00,-11.45,-31.90,-91.54:99.0:-0.48,-24.42,-1000.00,-10.74,-0.18,-30.25:-0.00,-29.09,-1000.00,-11.99,-3.44,-33.45:34 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1 791801 CNV_1_791801_893718 T <CN0>,<CN2> . 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1 833820 CNV_1_833820_910074 T <CN0>,<CN2> . 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1 833820 CNV_1_833820_921749 T <CN2> . 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I convert it to
FID IID CHR BP1 BP2 TYPE SCORE SITES
CP1600001 CP1600001 1 790997 830957 3 0 0
CP1600002 CP1600002 1 790997 830957 2 0 0
then I run
plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --cnv-make-map
plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --map plink.cnv.map --fam genomestrip.fam
plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --map plink.cnv.map --fam genomestrip.fam --cnv-intersect glist-hg38.dms --cnv-test-region --mperm 10000
the result is
$head plink.cnv.regional.summary.mperm
CHR REGION EMP1 EMP2
1 DDX11L1 1 1
1 WASH7P 1 1
1 MIR6859-1 1 1
1 MIR1302-2 1 1
1 FAM138A 1 1
1 OR4F5 1 1
1 LOC729737 1 1
1 MIR6859-1 1 1
1 FAM138D 1 1
Which step did I do wrong？
Best，
Maggie
I'm using development build (April 16) on Linux 64-bit. When I typed in plink2 --genome, I got
PLINK v2.00a2LM 64-bit Intel (16 Apr 2018) www.cog-genomics.org/plink/2.0/
(C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink2.log.
Options in effect:
--genome
Start time: Wed Apr 18 10:01:28 2018
Error: Unrecognized flag ('--genome').
For more info, try 'plink2 --help [flag name]' or 'plink2 --help | more'.
According to the documentation (https://www.cog-genomics.org/plink2/ibd), --genome should be available.
tl;dr - it would be useful if there were an option for using D' instead of correlation for --flip-scan.
--flip-scan is a useful tool in quality control for identifying flipped ambiguous SNPs when component parts of a GWAS have been genotyped separately. It can also be used to identify variants that have been miscalled during genotyping, as they (may) depart from the expected pattern of LD with neighbouring SNPs. To some extent, this is captured by --flip-scan's current correlation-based measure. However, D' might be a more useful measure here, as it is more sensitive to the presence of unlikely haplotypes. As such, it would be useful if --flip-scan had a D' mode as well.
Ideally, the output would be a variant of that from --flip-scan verbose
CHR_INDX Chromosome code
SNP_INDX Index variant identifier
BP_INDX Index variant base-pair coordinate
A1_INDX Index variant allele 1
SNP_PAIR Second variant identifier
BP_PAIR Second variant base-pair coordinate
A1_PAIR Second variant allele 1
D_PRIME_A Case-only D'
D_PRIME_U Control-only D'
The --a2-allele and --a1-allele command seem to not recognize tab separators. Is that expected?
Hi,
It would be nice to have a --indep-r2, (or --indep-pairwise dprime) that selects tag SNPs based on the real (haplotype-based) r^2.
Rationale:
Anyway, thanks for this great software.
Is it possible that PLINK2 python API can support a functionality to write multiple variants?
PgenReader currently has read_alleles_list, read_alleles_range, etc. and they are pretty useful. It would be great if there are some similar functions for PgenWriter as well.
Hello,
On my dataset (available upon request):
plink --bfile pair485_486 --ld 485 486
PLINK v1.90b2p 64-bit (22 May 2014) https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink.log.
16047 MB RAM detected; reserving 8023 MB for main workspace.
2 variants loaded from .bim file.
279 people (0 males, 0 females, 279 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Individual-major .bed file detected. Transposing to SNP-major form.
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Total genotyping rate is 0.795699.
2 variants and 279 people pass filters and QC.
Note: No phenotypes present.
--ld 485 486:
R-sq = 0.0840844 D' = 0.335014
Haplotype Frequency Expectation under LE
--------- --------- --------------------
CG 0.027563 0.006336
TG 0.063346 0.084573
CC 0.042134 0.063361
TC 0.866957 0.845730
In phase alleles are CG/TC
The r2 and D' are correct (i.e. same value as computed by myself or SNPRelate).
But if I do:
plink --bfile pair485_486 --r2 dprime --ld-window-r2 0
I get
CHR_A BP_A SNP_A CHR_B BP_B SNP_B R2 DP
1 184100503 485 1 184244493 486 0.0277044 0.288944
The values are totally different, and if I understood correctly the documentation they should not.
Hi,
when running as such
plink --bfile plink --remove-cluster-names SomePop --make-bed --out newplink --family
The call ends up with a segfault (tested on several datasets). It seems to take a very looooong time to get there though.
Easy work around is to
grep SomePop plink.fam > SomePop.indiv
and then just use
plink --remove SomePop.indiv
but I figured I should tell you about the bug.
Thanks for the software btw :)
Hey - I loving the speed ups with the new plink. I wish I had this back in 08!
I'm trying to extract chrY variants from high quality females. Independent of PAR I get lot's of artefacts on exomes which are causing problems.
Calculating missing or trying to filter on missing doesn't seem to work with small datasets (n=4). That or it could be due to the handling of chrY on females. Ideas?
# create the input ideally with --maf 1e-9 and --geno 1e-9
#plink --bfile xxx --chr 24 --keep high_confidence_females.txt --make-bed --out test1
# confirm that there are a mix of missing and variable positions
plink --bfile test1 --recode A --out test2
# missing/geno filtering doesn't work
plink --bfile test1 --chr 24 --geno 0.000001 --recode A --out test2
plink --bfile test1 --chr 24 --geno 0.999999 --recode A --out test2
# yup calculating missing is giving nan
plink --bfile test1 --chr 24 --miss --out test2
Command of type:
plink --bfile plink --genome full
Produces plink.genome file where all values on column IBS0 are constant depending on the input file. It's probably an output formatting issue since the other numbers match with old plink.
The Makefile appears to assume that the zlib library is located in the current directory
g++ -Wall -O2 plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c -m32 -o plink -L/usr/lib64/atlas -llapack -lcblas -latlas -lm -lpthread -L. zlib-1.2.8/libz.so.1.2.8
g++: error: zlib-1.2.8/libz.so.1.2.8: No such file or directory
It seems it might be better to use the system's zlib library.
Sorry to create this issue here, but there are no "contact" links on the cog-genomics.org site.
I saw Steven Hsu's talk on this study over a year ago, and I'm very curious about it. I notice that the main page of the site hasn't had any "news" items in over two years. How is it going?
If you could pass this message on to the right person, I'd appreciate it!
Hello,
I'm following this paper for QC filtering, but I'm running into an issue when I run this:
plink --bfile 00_data/hgdp –-genome --out 01_QC/03_duplication/hgdp
It outputs this error:
Error: --bfile accepts at most 1 parameter.
But I don't understand why I'm receiving that error since I specified the prefix within the 00_data folder?
I am not sure this is an issue with plink or with the BCF file or if the issue has been fixed, but here is a little discrepancy I found.
The BCF line for the variant is
22 16050654 10 A <CN0>,<CN2>,<CN3>,<CN4> 100 PASS AC=0,0,3,1;AF=0.00179712,0.0173722,0.119609,0.00399361;AN=40;CS=DUP_gs;END=16063474;NS=20;SVTYPE=CNV;DP=22545;ASN_AF=0,0,0,0;AMR_AF=0,0.0101,0.219,0.0072;SAS_AF=0.0082,0.1094,0.002;EUR_AF=0,0.007,0.0944,0.003;EAS_AF=0.001,0.0169,0.2361,0.0099;AFR_AF=0.0061,0.0363,0.0053,0;SAN_AF=0,0,0,0 GT:DP 3|0:4 0|0:7 0|0:7 0|0:11 0|0:11 0|0:11 0|4:5 0|0:11 0|0:10 0|3:16 0|0:1 0|0:14 0|0:6 0|0:9 0|3:10 0|0:13 0|0:1 0|0:9 0|0:4 0|0:7And the result of the command
~/src/plink2/plink \
--bfile test.bcf.plink \
--freqwas
22 10 <CN3> A 0.07895 38Should there be another line for <CN4>?
I converted the BCF to BED using the command
~/src/plink2/plink \
--bcf test.bcf \
--make-bed \
--out test.bcf.plink \
--allow-extra-chrAnd my version info is
~/src/plink2/plink --version
PLINK v1.90b2c 64-bit (29 Jul 2014)Got following result from "--genome full gz" . Z2 (and PI_HAT) is calculated wrong. Both of them should be about 1.0. The error is clear since Z0+Z1+Z2 < 1.0
using commit f7b55fc
FID1 IID1 FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT PHE DST PPC RATIO IBS0 IBS1 IBS2 HOMHOM HETHET
c990_1_10191NV c990_1_10191NV THL COROG438000 UN NA 0.0002 0.0000 0.0000 0.0000 0 0.999981 1.0000 4104.0000 1 1 79998 1.0000 4104.0000
Hi,
I tried to update the Home Brew recipe to install Plink2 (https://github.com/Homebrew/homebrew-science/pull/5243). I have linked to you commit 96f3637 as the source for version b3.46 however this is not a preferred option.
Is it possible to tag releases so that GitHub can create a tarball automatically for that release?
Cheers!
It just leaves an empty file. This is for plink2 (e.g., PLINK v1.90b3h). My command looks like the following.
plink \
--vcf my.vcf.gz \
--snps-only \
--keep-allele-order \
--keep samples.2.keep \
--geno 0.05 \
--r2 dprime with-freqs \
--ld-window-r2 0.0 \
--ld-window 1000000 \
--ld-window-kb 1000000 \
--ld-snp rsID_1232152 \
--out my.output
If I manually excluded the samples containing ./. using --remove, then it seems to work.
Hello! I am using --test-missing to compare differential missingness in variants between cases vs. controls. I have ~200,000 variants that ought to be compared, but the .missing result file contains only ~77,000 variants with reported frequencies.
These results have previously been pruned for excessive missingness, heterogeneity in individuals, etc.
I am running PLINK v1.90b4.6 64-bit (15 Aug 2017) on Linux Red Hat Enterprise. Relevant output from the --test-missingcommand:
196849 variants loaded from .bim file.
1487 people (739 males, 748 females) loaded from .fam.
1487 phenotype values loaded from .fam.
Before main variant filters, 1083 founders and 404 nonfounders present.
Warning: 1039 het. haploid genotypes present (see
merged_QCd_batchcomparison.hh ); many commands treat these as
missing.
Total genotyping rate is 0.999216.
196849 variants and 1487 people pass filters and QC.
Among remaining phenotypes, 508 are cases and 979 are controls.
Writing --test-missing report to merged_QCd_batchcomparison.missing
... done.
Any ideas why the report is truncated?
I'm struggling getting some illumina genotypes to load. I've converted the gtreports to lgen format but keep getting the 3+ allele error. In the example below all that's there is A and 0. Specifying --missing-genotype 0 didn't seem to help.
plink --lfile mega
Error: Variant '1:10001102-G-T' in .lgen file has 3+ different alleles
This was using code from Feb 2016. Using a version from 2014 worked.
I have a pipeline that generates a ped/map file for each sample using an Illumina gtc file and a python script that I wrote. I then use plink --file samp1 --merge-list samps2_n.txt --make-bed --out AllSamps to merge all of the genotypes together. I have found a few instances when the genotypes in the merged bed file are not 100% concordant with the genotypes in the original ped files. It seems to only happen if samples are in a particular order in the --merge-list file, though I can't figure out if there is a pattern as to when it happens.
I have been able to replicate this bug using both "PLINK v1.90b4.10 64-bit (3 Nov 2017)" and "PLINK v1.90b3.32 64-bit (24 Feb 2016)".
After the merge I checked concordance of the original ped file with the merged file using --merge-mode 7 and the concordance for 6 samples looked like this:
SC112442_PB100119_F03.concordance.log:674909 concordant, for a concordance rate of 0.970771.
SC112445_PB100119_E09.concordance.log:683633 concordant, for a concordance rate of 0.983495.
SC197867_PB100119_D10.concordance.log:687412 concordant, for a concordance rate of 0.989207.
SC198277_PB100119_E10.concordance.log:689111 concordant, for a concordance rate of 0.991734.
SC198278_PB100119_F10.concordance.log:690717 concordant, for a concordance rate of 0.993527.
SC198302_PB100119_H01.concordance.log:695791 concordant, for a concordance rate of 1.So for the 6 samples above, there was only 1 sample that was the expected 100% concordant. This was "samp1" in my example above.
I have files that I can send you to replicate the bug, though even compressed they seem to be too big to attach here.
Thanks,
Eric
I've been generating large maps of kb-aggregated pairwise LD r^2 values from the 1000 genomes project. The new implementation in plink-1.9 is blazingly fast :), but I keep getting a strange "doubling" distortion effect in the lower half of the matrix. It extent of the effect is different in --bin and --bin4 mode, and I saw it in --gz mode as well. I get the right result using the text dump LD matrix from plink-1.07. I've put together a repo that reproduces the problem:
Currently it is possible to add a gz modifier to --genome to create compressed output. I think it would be beneficial with a gz modifier, when generating basic statistics with --missing, --freq, --hardy and --het.
I am not sure how to get around this issue.
time ./plink --make-bed --vcf foo.vcf.gz --out foo.vcf.gz.plink --allow-extra-chr --vcf-idspace-to _
PLINK v1.90b3d 64-bit (10 Feb 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to foo.vcf.gz.plink.log.
129004 MB RAM detected; reserving 64502 MB for main workspace.
Error: Multiple instances of '_' in sample ID.
I am trying to make a bed file from a 1000 genomes phase 3 bam file, and it seg faults after about 42 minutes.
The version is:
$ plink
PLINK v1.90b2c 64-bit (29 Jul 2014)The command was:
$ plink \
--make-bed \
--bcf ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf \
--out ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink \
--allow-extra-chrThe output was:
PLINK v1.90b2c 64-bit (29 Jul 2014) https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.log.
32054 MB RAM detected; reserving 16027 MB for main workspace.
--bcf: 84739k variants complete.
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.bed
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.bim
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.fam
written.
84739846 variants loaded from .bim file.
2504 people (0 males, 0 females, 2504 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.nosex
.
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Total genotyping rate is 0.980324.
84739846 variants and 2504 people pass filters and QC.
Note: No phenotypes present.
--make-bed to
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.bed
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.bim
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.fam
Segmentation fault (core dumped)There were a number of temp files created, here are their sizes and the source bcf size:
129G ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf
62K ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.fam
0 ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.log
2.0G ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.bim
50G ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.bed
40K ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.nosex
0 ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.bed
2.0G ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.bimI am happy to provide any other debug info, just let me know what you need.
Thanks,
Ryan
Hi,
I am trying to export a portion of bgen+sample to transposed .traw format:
plink2 --bgen inputfile.bgen --sample inputfile.sample --keep input.sample --maf 0.001 --export A-transpose --out test
it successfully exported bgen+sample to temporary psam+pgen+pvar but failed on calculating frequencies stage with error and exits:
Calculating allele frequencies... 0%
Error: Malformed .pgen file.
I got PLINK v2.00aLM 64-bit Intel (4 Nov 2017) and Ubuntu 16.04 LTS, previous PLINK v2.00aLM 64-bit Intel (16 Oct 2017) version works fine.
When a pair of SNPs', A and B, r2 > 0.2, which one will be removed?
Hi,
GCC 6 has not been released yet, but it's expected that GCC 6 will become the default compiler for Debian Stretch (next release). As reported by Martin Michlmayr, plink 1.9 fails to build [1] with GCC 6:
sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
...
make[2]: Entering directory '/<>'
g++ -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c -o plink -llapack -lcblas -latlas -lm -lpthread -ldl -lz
In file included from plink.c:19:0:
plink_common.h:62:19: error: expected unqualified-id before 'long'
#define int64_t long long
^plink_common.h:62:19: error: expected ';' before 'long'
plink_common.h:62:24: error: declaration does not declare anything [-fpermissive]
#define int64_t long long
^plink_common.h:61:20: error: expected unqualified-id before 'unsigned'
#define uint64_t unsigned long long
^plink_common.h:61:20: error: expected ';' before 'unsigned'
plink_common.h:61:34: error: declaration does not declare anything [-fpermissive]
#define uint64_t unsigned long long
^
You can see the full build log here [2].
Best regards,
Dylan
[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811910
[2] https://launchpadlibrarian.net/233688889/buildlog_ubuntu-xenial-amd64.plink1.9_1.90~b3b-150117-1_BUILDING.txt.gz
Hi,
Plink 1.9 is now in official Debian repository [1] but it fails to build [2-3] on some architectures (arm64, ppc64el, s390x, etc) due to a missing header (emmintrin.h).
So what do you think about this? Should I disable build for these architectures or it is possible to fix this missing header?
Best regards,
Dylan
[1] https://tracker.debian.org/pkg/plink1.9
[2] https://buildd.debian.org/status/package.php?p=plink1.9
[3] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=799471
Hi Christopher,
I have got some CNV results for about 1000 samples, and I followed the instructions http://zzz.bwh.harvard.edu/plink/cnv.shtml#reg-assoc on the website to perform a region-based association test. In the result there’s a EMP1 and EMP2.
As what it says on the web page,
EMP1 Empirical p-value, per region
EMP2 Empirical p-value, corrected for all tests
However, it is not very clear to me how EMP2 was calculated, by that I mean what method has been applied for multiple tests correction.
Base on my data results, the correction seems to be stringent.
I’ve looked at other sections on the web page but couldn’t find a clear answer.
Could you explain a little on that or please point me to the relevant resources.
Thank you very much.
Regards,
Ruqian
Possible bug: in short the snp '5504' is pruned out but should not.
plink --bfile g10 --indep-pairwise 10 1 0.6
(~ window of 10 snps, step by 1, min R2=0.6)
cat plink.prune.out
5299
5329
5364
5431
5500
5504
But the closest snp in LD with 5504 is 5505, with R2=0.55
plink --bfile g10 --r2 gz dprime --ld-window 1000 --ld-window-r2 0.5
zcat plink.ld.gz
CHR_A BP_A SNP_A CHR_B BP_B SNP_B R2 DP
10 35833269 5285 10 35908553 5286 0.629441 1
10 44234390 5299 10 44236876 5300 0.859837 1
10 59232437 5329 10 59239732 5330 0.736516 0.959105
10 67462827 5363 10 67472107 5364 0.752807 0.9897
10 85763376 5430 10 85766574 5431 0.735795 1
10 109392397 5500 10 109393124 5501 0.684211 0.989152
10 110105576 5504 10 110110936 5505 0.550636 1
extra check:
plink --bfile g10 --ld 5504 5505
PLINK v1.90b2p 64-bit (27 May 2014) https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink.log.
16047 MB RAM detected; reserving 8023 MB for main workspace.
359 variants loaded from .bim file.
279 people (0 males, 0 females, 279 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Total genotyping rate is 0.996805.
359 variants and 279 people pass filters and QC.
Note: No phenotypes present.
--ld 5504 5505:
R-sq = 0.550636 D' = 1
Haplotype Frequency Expectation under LE
--------- --------- --------------------
GG -0 0.180072
TG 0.469534 0.289462
GA 0.383513 0.203440
TA 0.146953 0.327026
In phase alleles are GA/TG
Did I miss something ?
Dataset available upon request, I do not know how to attach it to the issue.
Hi
PLINK v1.90b5 gives an error when I try to make just a family file:
PLINK v1.90b5 64-bit (14 Nov 2017)
Options in effect:
--fam dos_pts_PROM_mix_am-qc.hg19.ch.fl.chr10_027_030.out.dosage.fam
--make-just-fam
--memory 500
--out dos_pts_PROM_mix_am-qc.hg19.ch.fl.chr10_027_030
Start time: Mon Dec 4 21:48:55 2017
Random number seed: 1512420535
64384 MB RAM detected; reserving 500 MB for main workspace.
3451 people (0 males, 3451 females) loaded from .fam.
3451 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 3414 founders and 37 nonfounders present.
Error: No variants remaining.
End time: Mon Dec 4 21:48:55 2017
This doesn't occur in an earlier version,
PLINK v1.90b3y 64-bit (4 Nov 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to test2.log.
Options in effect:
--fam dos_pts_PROM_mix_am-qc.hg19.ch.fl.chr9_141_144.out.dosage.fam
--make-just-fam
--memory 500
--out test2
32096 MB RAM detected; reserving 500 MB for main workspace.
3451 people (0 males, 3451 females) loaded from .fam.
3451 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 3414 founders and 37 nonfounders present.
Among remaining phenotypes, 1698 are cases and 1753 are controls.
--make-just-fam to test2.fam ... done.
I am guessing that --allow-no-vars would function as a work-around.
Also, is it possible to export a new .fam file when you filter down a dosage file?
e.g. to get a new family file after removing subjects:
plink --dosage filename.fam --fam filename.fam --remove remove.subjects --write-dosage --out dose_revised
Thanks
Adam
Command: "plink --bfile input --pheno alt.pheno --assoc"
gives different results for 1.07 and 1.9 with 1.9 giving wrong ones. At least for 1,2,-9 coded case/control phenotypes, the values from alt.pheno are not used in the association calculation. Instead, the original phenotype from input is used.
The alt.pheno file is read, as '--all-pheno' gives the correct name of the phenotype but the phenotype values are lost somewhere.
Dear Chang,
I am using the following command for gwas analysis.
plink --dosage $gprobs.file --fam $fam --covar $cov --covar-name PC1-PC5 --out $out
Does the BETA column in the output file represents the regression coefficient or the OR value? Is the SE column for the effect or for the OR? I tried to search the answers in the source code but haven't found the clue.
Thank you very much in advance.
Best,
Siyang
I'm seeing a duplicate ID error with the following vcf snippet. It looks like the set-missing-var-id isn't respecting REF/ALT order?? Easy enough to just add the ideas in bash.
plink --vcf test.vcf --set-missing-var-ids @:#_\$1_\$2 --make-bed --out test --double-id --keep-allele-order
Hi,
I called CNV using GenomeSTRiP software, I analyzed the CNV data via plink(v1.07) --gfile command,
and in the only results plink.gvar.summary FIELD and VALUE columns , what is the meaning of CNV yes or no?
What to do to get other information like the P and OR value from Basic case/control association test ？
Thank you
Best
Hi,
I am involved in Debian Med project which provide a GNU/Linux distribution for biomedical research. I am making a package of plink2 [1] for integration in official Debian repository, but as you know, there is a name clash with plink from ssh clone putty. So, to avoid the name clash with the first plink, plink2 and plink from ssh clone putty, maybe it could be useful to change the default name of the binary to plink2 or something like that.
At http://bugs.debian.org/503367 and http://bugs.debian.org/771154#25 you can read the full discussion about a name clash between one component of the frequently used ssh software putty and plink.
Best regards,
Dylan
(I am new to using plink and not formally trained in bioinformatics), first time trying to use plink it was connecting to web for a long time without anything happening, so i tried --noweb. Without realizing my error I am now stuck. Plink hangs and I can not write any commands, please advise!
See below where it gets stuck
/Users/linnmaristorengen/plink_mac/plink ; exit;
PLINK v1.90b5.2 64-bit (9 Jan 2018) www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3
plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
plink --help {flag name(s)...}
Commands include --make-bed, --recode, --flip-scan, --merge-list,
--write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
--hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
--blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
--rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
--model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
--make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
--meta-analysis, --epistasis, --fast-epistasis, and --score.
'plink --help | more' describes all functions (warning: long).
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
[Process executed]
Hi,
I converted my .cvf file into .bed/.fam/.bim format. For that I had to use --const-fid 0 because I was having this error message: Multiple instances of '_' in sample ID.
Then, all the families ID (FID) were set to '0'.
This is, however, causing me problems when I try to use Mega2, which throw me an error message because all FIDs are 0 and this is wrong because Mega2 is reading that all individuals belong to the same family. Anyway, what happens is that I need to edit FID so that each individuals as an unique FID (i.e FAM1, FAM2, FAM3..etc). Doing so, Mega2 will understand that all the individuals are unrelated (and hopefully I won't receive any error messages!).
I tried what it is explained here: (in the section 'update individuals information'). Specifically, I prepared a .txt file with four columns: old FID, old IID, new FID, new IID. It looks like this (only three first rows):
0 NWZ_106801_P03_WH01 FAM1 NWZ:106801:P03:WH01
0 NWZ_106801_P01_WD11 FAM2 NWZ:106801:P01:WD11
0 NWZ_106801_P03_WG01 FAM3 NWZ:106801:P03:WG01
Then I used this: $ plink2 -file myplink --update-ids EditFIDandIID.txt --make-bed --out myplinkRFfids
and this was what I got:
PLINK v1.90b3 64-bit (11 Jan 2015) https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to myplinkRFfids.log.
8192 MB RAM detected; reserving 4096 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (3412 variants, 265 people).
--file: myplinkRFfids-temporary.bed + myplinkRFfids-temporary.bim +
myplinkRFfids-temporary.fam written.
3412 variants loaded from .bim file.
265 people (0 males, 0 females, 265 ambiguous) loaded from .fam.
Ambiguous sex IDs written to myplinkRFfids.nosex .
--update-ids: 1 person updated.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 265 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.99727.
3412 variants and 265 people pass filters and QC.
Note: No phenotypes present.
The problem is that this just updated 1 individuals!, as also showed in the .fam when I open it:
FAM1 NWZ:106801:P03:WH01 0 0 0 -9
0 NWZ_106801_P01_WD11 0 0 0 -9
0 NWZ_106801_P03_WG01 0 0 0 -9
Does anyone knows what am I doing wrong? and what can I do to update FID of all the individuals successfully?
Thanks in advance,
Ángela Parody-Merino
cleanup_chrom_info(&chrom_info);
is deallocating memory that has already been deallocated.
$ gdb ../plink-ng/plink
GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.launchpad.net/gdb-linaro/>...
Reading symbols from /blah/plink-ng/plink...done.
(gdb) set args --vcf gdap_pilot.vcf.gz --memory 8000 --make-bed --out gdap_pilot --set-missing-var-ids @:#[b38]$1,$2 --autosome-xy --allow-extra-chr --double-id --biallelic-only --update-sex ../meta/gdap_pilot.sex --split-x b38 --within ../meta/gdap_pilot.clusters
(gdb) run
Starting program: /blah/plink-ng/plink --vcf gdap_pilot.vcf.gz --memory 8000 --make-bed --out gdap_pilot --set-missing-var-ids @:#[b38]$1,$2 --autosome-xy --allow-extra-chr --double-id --biallelic-only --update-sex ../meta/gdap_pilot.sex --split-x b38 --within ../meta/gdap_pilot.clusters
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
PLINK v1.90p 64-bit (8 Mar 2016) https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to gdap_pilot.log.
Options in effect:
--allow-extra-chr
--autosome-xy
--biallelic-only
--double-id
--make-bed
--memory 8000
--out gdap_pilot
--set-missing-var-ids @:#[b38],
--split-x b38
--update-sex ../meta/gdap_pilot.sex
--vcf gdap_pilot.vcf.gz
--within ../meta/gdap_pilot.clusters
257853 MB RAM detected; reserving 8000 MB for main workspace.
--vcf: gdap_pilot-temporary.bed + gdap_pilot-temporary.bim +
gdap_pilot-temporary.fam written.
(2996245 variants skipped.)
35286491 variants loaded from .bim file.
12822357 missing IDs set.
133 people (0 males, 0 females, 133 ambiguous) loaded from .fam.
Ambiguous sex IDs written to gdap_pilot.nosex .
--update-sex: 133 people updated.
--within: 5 clusters loaded, covering a total of 133 people.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 133 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Warning: 1340294 het. haploid genotypes present (see gdap_pilot.hh ); many
commands treat these as missing.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.
Total genotyping rate is 0.985164.
35286491 variants and 133 people pass filters and QC.
Note: No phenotypes present.
--make-bed to gdap_pilot.bed + gdap_pilot.bim + gdap_pilot.fam ... done.
Program received signal SIGSEGV, Segmentation fault.
0x00000000004b23d7 in forget_extra_chrom_names (chrom_info_ptr=0x7fffffff59c0) at plink_common.c:4415
4415 free(nonstd_names[chrom_idx]);
Where the nonstd_names pointer itself is already invalid. Specifically (from another debugging session):
(gdb) print *chrom_info_ptr
$5 = {chrom_mask = 0x0, haploid_mask = 0x2aaaad7ae130, chrom_file_order = 0x2aaaad7ae240, chrom_fo_vidx_start = 0x2aaaad7ae2b0, chrom_idx_to_foidx = 0x2aaaad7ae320, nonstd_names = 0x2aaaad7b0350, nonstd_id_htable = 0x2aaaad7b43b0, chrom_ct = 25, species = 0,
xymt_codes = {23, 24, 25, 26}, max_code = 26, autosome_ct = 22, zero_extra_chroms = 0, name_ct = 2033, incl_excl_name_stack = 0x0, is_include_stack = 1, output_encoding = 0}
(gdb) print *0x2aaaad7b0350
Cannot access memory at address 0x2aaaad7b0350
(gdb) print *0x2aaaad7b43b0
Cannot access memory at address 0x2aaaad7b43b0
(gdb) print *0x2aaaad7ae2b0
Cannot access memory at address 0x2aaaad7ae2b0
I am trying to merge single chromosome files (converted to .bed after imputation to Thousand Genomes Phase 1), but running into a segfault in merge_fam_id_scan.
The following works:
$ plink --memory 4000 --bfile 58C_01 --bmerge 58C_02 --make-bed --out test
PLINK v1.90b3.38 64-bit (7 Jun 2016) https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to test.log.
Options in effect:
--bfile 58C_01
--bmerge 58C_02
--make-bed
--memory 4000
--out test
48251 MB RAM detected; reserving 4000 MB for main workspace.
1478 people loaded from 58C_01.fam.
1478 people to be merged from 58C_02.fam.
Of these, 0 are new, while 1478 are present in the base dataset.
711902 markers loaded from 58C_01.bim.
772778 markers to be merged from 58C_02.bim.
Of these, 772778 are new, while 0 are present in the base dataset.
Warning: Variants 'rs111748052|chr01|886817|886817|CATTTT' and
'rs10465241|chr01|886817|886817|T' have the same position.
Warning: Variants 'rs201179857|chr01|1036876|1036876|TA' and
'rs11578997|chr01|1036876|1036876|A' have the same position.
Warning: Variants 'rs144847714|chr01|3765424|3765424|GT' and
'rs10492943|chr01|3765424|3765424|T' have the same position.
1319 more same-position warnings: see log file.
Performing single-pass merge (1478 people, 1484680 variants).
Merged fileset written to test-merge.bed + test-merge.bim + test-merge.fam .
1484680 variants loaded from .bim file.
1478 people (739 males, 739 females) loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1478 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.868617.
1484680 variants and 1478 people pass filters and QC.
Note: No phenotypes present.
--make-bed to test.bed + test.bim + test.fam ... done.
But using --merge-list crashes with a segfault:
$ plink --memory 4000 --bfile 58C_01 --merge-list <(echo 58C_02) --make-bed --out test2
$ plink --memory 4000 --merge-list <(echo 58C_01; echo 58C_02) --make-bed --out test2
Both ways fail with the same gdb backtrace:
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /broad/compbio/aksarkar/.local/bin/plink...(no debugging symbols found)...done.
(gdb) target core core.22642
target core core.22642
[New Thread 22642]
[Thread debugging using libthread_db enabled]
Core was generated by `plink --memory 4000 --merge-list /dev/fd/63 --make-bed --out test2'.
Program terminated with signal 11, Segmentation fault.
#0 0x00000000008362b1 in strlen ()
(gdb) bt
bt
#0 0x00000000008362b1 in strlen ()
#1 0x000000000049ddbd in merge_fam_id_scan(char*, char*, unsigned int, unsigned long*, unsigned int*, unsigned int*, ll_entry_struct**, unsigned long long*, unsigned int*, unsigned int*, unsigned int*) ()
#2 0x00000000004c80cd in merge_datasets(char*, char*, char*, char*, char*, char*, char*, char*, char*, unsigned long long, unsigned int, unsigned int, unsigned long long, Chrom_info*) ()
#3 0x0000000000404101 in plink(char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, two_col_params_struct*, two_col_params_struct*, char*, char*, char*, char*, two_col_params_struct*, two_col_params_struct*, two_col_params_struct*, two_col_params_struct*, two_col_params_struct*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, unsigned int, double, double, double, double, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, int, char*, unsigned int, unsigned int, Chrom_info*, Oblig_missing_info*, Family_info*, double, double, unsigned int, unsigned int, double, double, double, double, double, double, double, double, unsigned long long, unsigned long long, unsigned long long, unsigned int, unsigned long, unsigned int, unsigned long, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, double, double, Homozyg_info*, Cluster_info*, unsigned int, unsigned int, Set_info*, Ld_info*, Epi_info*, Clump_info*, Rel_info*, Score_info*, uns---Type <return> to continue, or q <return> to quit---
igned int, unsigned int, unsigned int, unsigned int, int, int, int, char*, char*, char*, range_list_struct*, unsigned int, unsigned int, range_list_struct*, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, unsigned int, double, unsigned int, unsigned int, range_list_struct*, range_list_struct*, double, double, double, unsigned int, double, unsigned int, Aperm_info*, unsigned int, unsigned long, unsigned int, double, unsigned int, double, range_list_struct*, unsigned int, unsigned int, unsigned int, int, ll_str_struct**) ()
#4 0x0000000000415fdf in main ()
Hello,
I'm unsure of how to interpret and proceed with remaining QC steps because of this error? I wanted to create a new bed file to exclude hgdp data whose SNPs were not found in 1000 Genome Phase 3 Chromosome 1 population data.
Code:
plink --noweb --bfile 00_data/hgdp -extract 00_data/1000GP_Phase3/genetic_map_chr1_combined_b37.txt --make-bed --out 01_QC/04_div_ancestry/hgdp.1000-snps
Error:
660873 variants loaded from .bim file. 1043 people (673 males, 370 females) loaded from .fam. Error: No variants remaining after --extract.
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