Comments (10)
traxexx
commented on May 28, 2024
1
Going to make idxdepth ignore ALT contigs.
from paragraph.
traxexx
commented on May 28, 2024
1
Binned coverage for bam files is disabled in idxdepth. That's why you cannot get binnedcov.txt for your bam file. I have no idea why @pkrusche applies this. While waiting for his reply, I'll try to figure it out.
from paragraph.
dantaki
commented on May 28, 2024
I am getting the same error too
[2019-07-15 16:42:23.776] [idxdepth] [12150] [info] Thread 46971021932288 done estimating depth for chrUn_JTFH01001987v1_decoy ; DP = 579.61 after 5230 us
[2019-07-15 16:42:23.776] [idxdepth] [12150] [info] Thread 46971021932288 estimating depth for chrUn_JTFH01001996v1_decoy
[2019-07-15 16:42:25.712] [idxdepth] [12152] [info] Thread 46971442169600 done estimating depth for chrUn_JTFH01001989v1_decoy ; DP = 0 after 4112.74 us
[2019-07-15 16:42:25.712] [idxdepth] [12152] [info] Thread 46971442169600 estimating depth for chrUn_JTFH01001997v1_decoy
[2019-07-15 16:42:25.748] [idxdepth] [12147] [info] Thread 46971015628544 done estimating depth for chrUn_JTFH01001990v1_decoy ; DP = 0 after 4109.9 us
[2019-07-15 16:42:25.748] [idxdepth] [12147] [info] Thread 46971015628544 estimating depth for chrUn_JTFH01001998v1_decoy
[2019-07-15 16:42:25.948] [idxdepth] [12153] [info] Thread 46971444270848 done estimating depth for chrUn_JTFH01001992v1_decoy ; DP = 0.44 after 3825.24 us
[2019-07-15 16:42:25.948] [idxdepth] [12153] [info] Thread 46971444270848 estimating depth for HLA-A*01:01:01:01
[2019-07-15 16:42:25.968] [idxdepth] [12149] [info] Thread 46971019831040 done estimating depth for chrUn_JTFH01001991v1_decoy ; DP = 1.87 after 3982.76 us
[2019-07-15 16:42:25.968] [idxdepth] [12149] [info] Thread 46971019831040 estimating depth for HLA-A*01:01:01:02N
[2019-07-15 16:42:26.218] [idxdepth] [12154] [info] Thread 46971643496192 done estimating depth for chrUn_JTFH01001993v1_decoy ; DP = 0.03 after 2784.95 us
[2019-07-15 16:42:26.218] [idxdepth] [12154] [info] Thread 46971643496192 estimating depth for HLA-A*01:01:38L
[2019-07-15 16:42:26.244] [idxdepth] [12148] [info] Thread 46971017729792 done estimating depth for chrUn_JTFH01001994v1_decoy ; DP = 2.34 after 2709.57 us
[2019-07-15 16:42:26.244] [idxdepth] [12148] [info] Thread 46971017729792 estimating depth for HLA-A*01:02
[2019-07-15 16:42:26.482] [idxdepth] [12151] [info] Thread 46971240843008 done estimating depth for chrUn_JTFH01001995v1_decoy ; DP = 2.66 after 2946.74 us
[2019-07-15 16:42:26.482] [idxdepth] [12151] [info] Thread 46971240843008 estimating depth for HLA-A*01:03
[2019-07-15 16:42:26.488] [idxdepth] [12150] [info] Thread 46971021932288 done estimating depth for chrUn_JTFH01001996v1_decoy ; DP = 1.13 after 2711.84 us
[2019-07-15 16:42:26.488] [idxdepth] [12150] [info] Thread 46971021932288 estimating depth for HLA-A*01:04N
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoll
Here's my argument
idxdepth -b NA19240.alt_bwamem_GRCh38DH.20150715.YRI.high_coverage_markedDupsRemoved.bam \
-o NA19240.paragraph_cov.txt \
-O NA19240.paragraph_binnedcov.txt \
-r GRCh38_full_analysis_set_plus_decoy_hla.fa \
--threads 8
Is there a way to not process the decoy contigs?
Thank you.
from paragraph.
dantaki
commented on May 28, 2024
I tried to use these options
--autosome-regex '(chr)?[1-9][0-9]?' --sex-chromosome-reg '(chr)?[XY]?'
But it started to process the ALT contigs in hg38.
[2019-07-16 07:00:39.498] [idxdepth] [34604] [info] Thread 47330071938816 done estimating depth for chr22 ; DP = 52.7 after 52444 us
[2019-07-16 07:00:39.498] [idxdepth] [34604] [info] Thread 47330071938816 estimating depth for chr1_KI270706v1_random
[2019-07-16 07:00:44.000] [idxdepth] [34604] [info] Thread 47330071938816 done estimating depth for chr1_KI270706v1_random ; DP = 86.97 after 4501.77 us
[2019-07-16 07:00:44.000] [idxdepth] [34604] [info] Thread 47330071938816 estimating depth for chr1_KI270707v1_random
[2019-07-16 07:00:45.477] [idxdepth] [34600] [info] Thread 47329517483776 done estimating depth for chrM ; DP = 15677.6 after 17895.2 us
[2019-07-16 07:00:45.477] [idxdepth] [34600] [info] Thread 47329517483776 estimating depth for chr1_KI270708v1_random
[2019-07-16 07:00:46.694] [idxdepth] [34599] [info] Thread 47329515382528 done estimating depth for chr18 ; DP = 80.98 after 70156.3 us
[2019-07-16 07:00:46.694] [idxdepth] [34599] [info] Thread 47329515382528 estimating depth for chr1_KI270709v1_random
[2019-07-16 07:00:48.232] [idxdepth] [34601] [info] Thread 47329602176768 done estimating depth for chr17 ; DP = 65.13 after 74335.1 us
[2019-07-16 07:00:48.233] [idxdepth] [34601] [info] Thread 47329602176768 estimating depth for chr1_KI270710v1_random
[2019-07-16 07:00:51.749] [idxdepth] [34604] [info] Thread 47330071938816 done estimating depth for chr1_KI270707v1_random ; DP = 89.22 after 7748.92 us
[2019-07-16 07:00:51.749] [idxdepth] [34604] [info] Thread 47330071938816 estimating depth for chr1_KI270711v1_random
from paragraph.
dantaki
commented on May 28, 2024
Thanks please update this thread. For now I am using bedtools genomecov
from paragraph.
traxexx
commented on May 28, 2024
v2.3 released with idxdepth excluding ALT contig as default. Let me know if this problem still exists with v2.3.
from paragraph.
dantaki
commented on May 28, 2024
Seems to work now, except I do not see the -O NA19240.paragraph_binnedcov.txt output.
It skips the ALT contigs but I get this error
[2019-07-29 09:54:42.694] [idxdepth] [27225] [critical] BAM index reading not available yet.
The NA19240.paragraph_cov.txt is present and looks good.
Thanks for quickly addressing this issue!
from paragraph.
pkrusche
commented on May 28, 2024
Estimating coverage from a CRAM index is done by proxy (number of bytes in chunk), which is easy to implement (the method was shown here: https://github.com/brentp/goleft/tree/master/indexcov). On a BAM index this should be possible also, but will have to be done differently -- it wasn't implemented because there was no need when I wrote this (all relevant files were CRAMs).
from paragraph.
dantaki
commented on May 28, 2024
Ok I thought the "binned" coverage was something similar to CNVnator, which calculates read depth in bins of a specific (user-defined) length.
So it seems to not be relevant to this concept, the output for idxdepth is fine now. Thanks for all your help!
from paragraph.
traxexx
commented on May 28, 2024
Thank you all for your discussion. v2.4 dded another warning message in idxdepth for BAM file for this issue.
from paragraph.
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