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ACEnglish avatar ACEnglish commented on June 24, 2024

We currently only recommend using Truvari to compare variants ≥ ~20bp or variants ≥5bp in narrowly defined regions such as TRs. We have in our development roadmap implementing and fully validating <5bp variants.

However, it is possible to compare smaller variants, it just may create inaccurate results. Your parameters are close to what would be needed to test out tiny variant comparison.

  1. --sizemin shouldn't be less than --sizefilt. Either set both to 0 or just provide --sizemin 0 and --sizefilt is automatically set to 0.
  2. I would recommend keeping sequence similarity on by not providing --pctsim 0. Otherwise an e.g. T may match to an A. But if allowing these types of matches is part of your experiment. you can keep --pctsim 0
  3. The same thing goes for --pctsize. I would just leave the defaults.
  4. --sizemax is a ≤ limit, so 1bp INDELs are being analyzed by when given these parameters. That would also need to be set to 0 if you wanted to only look at SNVs.

That should get you a different answer. But again, we cannot vouch for its validity. The ability of Truvari to compare tiny variants should not be confused with any kind of proficiency.

Tools that are built for small variants include rtg vcfeval for all VCFs and vcfdist for phased VCFs.

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xiaomiyongyuan avatar xiaomiyongyuan commented on June 24, 2024

THANKS!
I have attempted it:
truvari bench -b "sorthg002benend.vcf.gz" -c "sorthg002benend.vcf.gz" --pctsim 0 -o out --sizemin 0 --sizefilt 0 --sizemax 0
This is my command. I want to test it using two identical files. If TP equals the total number of SVs, then it proves that my run is correct. However, after using the above command, I found that TP is still 0, which leaves me puzzled.My input VCF data body looks like this:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002
chr1 602113 . T TGCCCA 50 PASS platforms=3;platformnames=PacBio,10X,Illumina;datasets=3;datasetnames=CCS15kb_20kb,10XChromiumLR,HiSeq250x250;callsets=4;calls>
chr1 604358 . G C 50 PASS platforms=3;platformnames=PacBio,10X,Illumina;datasets=4;datasetnames=CCS15kb_20kb,10XChromiumLR,HiSeq250x250,HiSeqMatePair;ca>
chr1 604360 . T C 50 PASS platforms=3;platformnames=PacBio,10X,Illumina;datasets=4;datasetnames=CCS15kb_20kb,10XChromiumLR,HiSeq250x250,HiSeqMatePair;ca>
chr1 611317 . A G 50 PASS platforms=3;platformnames=PacBio,Illumina,10X;datasets=5;datasetnames=CCS15kb_20kb,HiSeqPE300x,10XChromiumLR,HiSeq250x250,HiSe>
chr1 631859 . CG C 50 PASS platforms=2;platformnames=PacBio,Illumina;datasets=4;datasetnames=CCS15kb_20kb,HiSeqPE300x,HiSeq250x250,HiSeqMatePair;callsets>

There might still be a little problem. I will try other methods! Thank you very much!

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xiaomiyongyuan avatar xiaomiyongyuan commented on June 24, 2024

2024-02-19 23:16:22,189 [INFO] Params:
{
"base": "sorthg002benend.vcf.gz",
"comp": "sorthg002benend.vcf.gz",
"output": "out",
"reference": null,
"giabreport": false,
"debug": false,
"prog": false,
"refdist": 500,
"pctsim": 0.0,
"buffer": 0.1,
"pctsize": 0.7,
"pctovl": 0.0,
"typeignore": false,
"use_lev": false,
"gtcomp": false,
"bSample": null,
"cSample": null,
"sizemin": 0,
"sizefilt": 0,
"sizemax": 0,
"passonly": false,
"no_ref": false,
"includebed": null,
"multimatch": false
}
2024-02-19 23:16:22,191 [INFO] Creating call interval tree for overlap search
2024-02-19 23:16:22,193 [INFO] 50 call variants in total
2024-02-19 23:16:22,193 [INFO] 46 call variants within size range (0, 0)
2024-02-19 23:16:22,194 [INFO] Matching base to calls
2024-02-19 23:16:22,211 [WARNING] No TP or FP calls in comp!
2024-02-19 23:16:22,211 [INFO] Parsing FPs from calls
2024-02-19 23:16:22,212 [WARNING] No TP or FP calls in comp!
2024-02-19 23:16:22,212 [INFO] Stats: {
"TP-base": 0,
"TP-call": 0,
"FP": 0,
"FN": 46,
"precision": 0,
"recall": 0,
"f1": "NaN",
"base cnt": 46,
"call cnt": 0,
"TP-call_TP-gt": 0,
"TP-call_FP-gt": 0,
"TP-base_TP-gt": 0,
"TP-base_FP-gt": 0,
"gt_concordance": 0
}
2024-02-19 23:16:22,212 [INFO] Finished bench

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ACEnglish avatar ACEnglish commented on June 24, 2024

Oh, it looks like you're using an older version of Truvari. Using v4.2.1 I ran truvari bench -s 0 -b tiny.vcf.gz -c tiny.vcf.gz -o delme on the below 157 variants and they all matched

    TP-base: 157,
    TP-comp: 157,
    FP: 0,
    FN: 0,
    precision: 1.0,
    recall: 1.0,
    f1: 1.0,
    base cnt: 157,
    comp cnt: 157,

VCF:

Details

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SVTYPE">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="SVLEN">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002.H1
chr1 688908 . G C 60 PASS . GT 0/0
chr1 688948 . G T 60 PASS . GT 0/0
chr1 689063 . T A 60 PASS . GT 0/0
chr1 689088 . A G 60 PASS . GT 0/0
chr1 689236 . G T 60 PASS . GT 0/0
chr1 689239 . G A 60 PASS . GT 0/0
chr1 689334 . T C 60 PASS . GT 0/0
chr1 689344 . G GA 60 PASS . GT 0/0
chr1 689436 . G A 60 PASS . GT 0/0
chr1 689520 . T C 60 PASS . GT 0/0
chr1 689541 . C A 60 PASS . GT 0/0
chr1 689749 . C G 60 PASS . GT 0/0
chr1 689761 . T TA 60 PASS . GT 0/0
chr1 689803 . G A 60 PASS . GT 0/0
chr1 689819 . C T 60 PASS . GT 0/0
chr1 689933 . A C 60 PASS . GT 0/0
chr1 689962 . C T 60 PASS . GT 0/0
chr1 689991 . T C 60 PASS . GT 0/0
chr1 690012 . T C 60 PASS . GT 0/0
chr1 690021 . C T 60 PASS . GT 0/0
chr1 690039 . G T 60 PASS . GT 0/0
chr1 690060 . A C 60 PASS . GT 0/0
chr1 690092 . C CT 60 PASS . GT 0/0
chr1 690098 . G T 60 PASS . GT 0/0
chr1 690136 . A G 60 PASS . GT 0/0
chr1 690169 . A G 60 PASS . GT 0/0
chr1 690272 . G C 60 PASS . GT 0/0
chr1 690344 . A G 60 PASS . GT 0/0
chr1 690432 . A G 60 PASS . GT 0/0
chr1 690714 . T A 60 PASS . GT 0/0
chr1 690854 . G A 60 PASS . GT 0/0
chr1 690941 . A G 60 PASS . GT 0/0
chr1 691056 . C CA 60 PASS . GT 0/0
chr1 691199 . G A 60 PASS . GT 0/0
chr1 691306 . CCT C 60 PASS . GT 0/0
chr1 691319 . T C 60 PASS . GT 0/0
chr1 691405 . A C 60 PASS . GT 0/0
chr1 692064 . C T 60 PASS . GT 0/0
chr1 692574 . T C 60 PASS . GT 0/0
chr1 692760 . T C 60 PASS . GT 0/0
chr1 693086 . A C 60 PASS . GT 0/0
chr1 693190 . C A 60 PASS . GT 0/0
chr1 693461 . G C 60 PASS . GT 0/1
chr1 693681 . C A 60 PASS . GT 0/0
chr1 694044 . T C 60 PASS . GT 0/0
chr1 694627 . T C 60 PASS . GT 0/0
chr1 695296 . G A 60 PASS . GT 0/0
chr1 695396 . A G 60 PASS . GT 0/0
chr1 695433 . T C 60 PASS . GT 0/0
chr1 696021 . C T 60 PASS . GT 0/0
chr1 696276 . C CA 60 PASS . GT 0/0
chr1 696741 . A C 60 PASS . GT 0/0
chr1 696779 . G A 60 PASS . GT 0/0
chr1 696851 . C G 60 PASS . GT 0/0
chr1 696869 . A G 60 PASS . GT 0/0
chr1 696963 . C G 60 PASS . GT 0/0
chr1 697028 . T C 60 PASS . GT 0/0
chr1 697051 . T C 60 PASS . GT 0/0
chr1 697250 . A G 60 PASS . GT 0/0
chr1 697586 . T C 60 PASS . GT 1/1
chr1 698202 . C T 60 PASS . GT 1/1
chr1 698667 . G A 60 PASS . GT 0/0
chr1 699030 . G A 60 PASS . GT 1/1
chr1 699033 . C T 60 PASS . GT 1/1
chr1 699078 . A G 60 PASS . GT 1/1
chr1 699236 . C T 60 PASS . GT 1/1
chr1 699298 . TG T 60 PASS . GT 1/1
chr1 699538 . C T 60 PASS . GT 1/1
chr1 700073 . C T 60 PASS . GT 0/0
chr1 700155 . C T 60 PASS . GT 1/1
chr1 700421 . G A 60 PASS . GT 0/0
chr1 700500 . A G 60 PASS . GT 0/0
chr1 700537 . A G 60 PASS . GT 1/1
chr1 700606 . A G 60 PASS . GT 0/0
chr1 700712 . T G 60 PASS . GT 1/1
chr1 700905 . T C 60 PASS . GT 0/0
chr1 700918 . T C 60 PASS . GT 0/0
chr1 700938 . G A 60 PASS . GT 1/1
chr1 701595 . G A 60 PASS . GT 0/0
chr1 702960 . G A 60 PASS . GT 0/0
chr1 702977 . C A 60 PASS . GT 0/0
chr1 703393 . C T 60 PASS . GT 1/1
chr1 703919 . T C 60 PASS . GT 0/0
chr1 704094 . A G 60 PASS . GT 0/0
chr1 704240 . C T 60 PASS . GT 1/1
chr1 704306 . A C 60 PASS . GT 1/1
chr1 704543 . A G 60 PASS . GT 1/1
chr1 704780 . T C 60 PASS . GT 0/0
chr1 705172 . T C 60 PASS . GT 0/0
chr1 705491 . A C 60 PASS . GT 1/1
chr1 705793 . C T 60 PASS . GT 0/0
chr1 705856 . A C 60 PASS . GT 0/0
chr1 706138 . T G 60 PASS . GT 0/0
chr1 707008 . T C 60 PASS . GT 0/0
chr1 707496 . C T 60 PASS . GT 0/0
chr1 707497 . G A 60 PASS . GT 0/0
chr1 707895 . G A 60 PASS . GT 1/1
chr1 708085 . C A 60 PASS . GT 1/1
chr1 708143 . C CA 60 PASS . GT 0/0
chr1 708448 . G A 60 PASS . GT 0/0
chr1 709509 . T C 60 PASS . GT 0/0
chr1 710579 . T TAAAGAACTGCCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS SVTYPE=INS;SVLEN=320 GT 1/1
chr1 710579 . T TAAAGAACTGCCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS SVTYPE=INS;SVLEN=344 GT 0/0
chr1 710579 . T TAAAGAACTGCCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS SVTYPE=INS;SVLEN=336 GT 0/0
chr1 710579 . T TAAAGAACTGCCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACAAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS SVTYPE=INS;SVLEN=320 GT 0/0
chr1 710579 . T TAAAGAACTGCCCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS SVTYPE=INS;SVLEN=319 GT 0/0
chr1 710856 . C G 60 PASS . GT 0/0
chr1 711235 . C T 60 PASS . GT 0/0
chr1 711761 . A G 60 PASS . GT 0/0
chr1 711958 . TTATATATTATATATCTATTATATATAATATTATATATCTATTATATATTATATATTGTATATCTATTACATATATATTATATATGTATTA T 60 PASS SVTYPE=DEL;SVLEN=90 GT 0/0
chr1 712048 . A ATATATAT 60 PASS . GT 1/1
chr1 712228 . C CT 60 PASS . GT 1/1
chr1 712344 . G A 60 PASS . GT 0/0
chr1 712480 . C T 60 PASS . GT 0/0
chr1 713463 . TATTA T 60 PASS . GT 0/0
chr1 713495 . A AAT 60 PASS . GT 0/0
chr1 713733 . C T 60 PASS . GT 1/1
chr1 713773 . TAA T 60 PASS . GT 0/0
chr1 713812 . A T 60 PASS . GT 0/0
chr1 714324 . GTAGAAGAATATGAGACATTTCCCTAATCATTATGTGTAATTACAATTACA G 60 PASS SVTYPE=DEL;SVLEN=50 GT 1/1
chr1 714355 . TATGTGTAATTACAATTACATAGAAGAATATGAGACATTTCCCTAATCATTATGTGTAATTACAATTACATATATATATGTAATTGTAATTACACATA T 60 PASS SVTYPE=DEL;SVLEN=97 GT 0/0
chr1 714679 . G A 60 PASS . GT 0/0
chr1 714717 . A G 60 PASS . GT 1/1
chr1 714817 . A T 60 PASS . GT 0/0
chr1 715674 . A G 60 PASS . GT 1/1
chr1 715769 . C T 60 PASS . GT 1/1
chr1 715831 . C CAAAAAAAA 60 PASS . GT 0/0
chr1 716477 . T C 60 PASS . GT 0/0
chr1 717447 . G GA 60 PASS . GT 0/0
chr1 717682 . TA T 60 PASS . GT 1/1
chr1 718138 . A AAG 60 PASS . GT 1/1
chr1 718346 . A G 60 PASS . GT 0/0
chr1 718642 . A C 60 PASS . GT 0/0
chr1 718949 . A G 60 PASS . GT 0/0
chr1 720012 . G A 60 PASS . GT 0/0
chr1 720654 . CT C 60 PASS . GT 1/1
chr1 720963 . A G 60 PASS . GT 0/0
chr1 721646 . G A 60 PASS . GT 0/0
chr1 721662 . G A 60 PASS . GT 0/0
chr1 721920 . G C 60 PASS . GT 0/0
chr1 722169 . T G 60 PASS . GT 0/0
chr1 722252 . GAGTCTC G 60 PASS . GT 1/1
chr1 722408 . G C 60 PASS . GT 1/1
chr1 722803 . A G 60 PASS . GT 0/0
chr1 723038 . A G 60 PASS . GT 0/0
chr1 724417 . C T 60 PASS . GT 0/0
chr1 724698 . G A 60 PASS . GT 1/0
chr1 724712 . A G 60 PASS . GT 0/1
chr1 724785 . A G 60 PASS . GT 0/0
chr1 724994 . CTTCTCCCAGGTGAAGCCATTTAATCCTTTCAGTTTGGGACGGAGTAAGGCCTTCCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACCGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAACCTCTTCCCGCCGGGTTCACGCCATTCTCCTGCCTCAGCCTTCCGGGTAGCTAGGATTACAGGTGGACGCTACCACGTCCGGCTAATTTTTGTATTTTTAGTACAGACGGGGCTTCATCATCTTGGCCAGGCTGATTTCGATCTCCTGACATCGTGATCTGCCTGCCTCCCCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGCCAAGGCCTGCTCCTCTTATCTATACCCCCTACCCCTGCAGCTGTGCCGGGGGAAAGCTGGGCAGTTTCCCTCCTCCGAGCCCCTGTACATACCATGAATTGTGGGACCTTCAGAGCTTTTCACTTTTCGGAAAATAGCTCCTGCTGGGGCTACAAGATGGAGTGTGAAGAGGGCCTTGGGCCACAGGGAGGCGCCTGTGGACTAGGGGGAGTTCATGCACCCCTTCTTTCCCCAGAGGGGCTGGACTCAGGTGAGTATGGGGGTGGGGGCTCCTGCACTTCGACACAGGCAGCGGGAGGGTTTTCTCCCCATTCCCTCTGCACTCCCAACTTGAGCTATACTTTTTAAGAAAGTGATTCACCCTGCCTTTGCCCCCTTCCCCAGAACAGAACACGTTGATCGTGGGCGATATTTTTCATTGTGCCAAAAAGTTGCCATGACCGTCATTAAACCTGTTTAACACCAAATAATAAGGAAAATAAAATAAAAAATTCGGGCTTGGCGCAGAAACTCACTCCAAATAAATTACCTATCAAAATATTTACATAATGGTGGAAATATTCCAAAATTCAATATTTTGGGATTTATACACAAAAGATAAACAAATTAGAGGCCAAGAGGCTGCCGGAAGGGAAAAACGGGGCCTGGAATGGCCGACGTGAGGAATGAGCTGGGCCTAAAGAGGCCACTGGCAGGCAGGAGCTGGACCTGCCGAAGTGGCCGAAAGGCAGGAGCTTTGGACTGGGGAGGCCGCAGTGAGGCGAGAGCTAGCTGGGCGTGGAGAGTCTGCTGTGAGGCCGAGGCCGAGGCCGGGCCCGTGCAGGCCTTCGAGAGGCAGGAGGCCGGGCCTGCAAAGGCCGACTGGAGATCAAGTTCTGCGCCTGAAGAGGCTGCCAAAAGTCAAAAGCGGGGCCTGGGAAGGCCGCCGAGAGCCATGAGCTGGGCTGGGCCGAAAGAGGCCACTGGGAGGCAGGAGGAGCTGGGCCTGGAGAGGCTGACTCGAGGAAGTTTTGCACCTGGAGAGGCCGTCGAGAGGACGGAGCTGGGCCCAGGGAGGCCGACTTGCTGCTCTTCCAGGCCCACTTCCAGGCCGACTTGAGGACGACTTGGGCCTGCAGAGGCCGCCGGGAGGCTGGAGCTAAGCCTGGAGAGACTGACTTCGGGACGATTTGGGCCTGCAGAGGCCGCCGGGAGGCCCAAGCTGGGCCTAGAGGAGCCCACCGACCGGAGGCCATTTGGGGCCTGCAGATGTCATCGGAGGGCCAGGAGCTGAGCCTGGAGAGGCCACCGCGAGGCCTGAGCTGGGCCTGGGGAGCTTGGCTTAGGGAAGTTGTGGGCCTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCGGCCTGGAGATGCAGCCGGGAGGAAGAGCTGGGCCCGGAGGGGGCGCCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCGCATTGCCCAGCTGTTCCTCCTGGCTGCATCTCCCACCTCCCAGCAAACAAGCTCTTTTGGCTCAGCTCCCGCCTGCGTTTGTAGACCCCGAAGTTTCTGCAACCAAGCTCTTCAGACCCACATCCCTTCTCCCAGTGACTGAACAGTCCCAGCTCCGGCTGGAGAAGGGCGTCTGCAGACCCCGCTGTTGCCTCCCAGGGGAGTCTCCAGGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTACCTCCCAGCAGCCCGAGTGCGATCCTGTTCCTCCCTCACGGT C 60 PASS SVTYPE=DEL;SVLEN=2184 GT 0/0
chr1 725051 . C CT 60 PASS . GT 1/0
chr1 725051 . CT C 60 PASS . GT 0/0
chr1 725086 . C G 60 PASS . GT 1/1
chr1 725985 . C T 60 PASS . GT 0/0
chr1 726152 . TGAGGCC T 60 PASS . GT 0/0
chr1 726649 . G A 60 PASS . GT 1/1
chr1 726821 . G A 60 PASS . GT 1/1

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xiaomiyongyuan avatar xiaomiyongyuan commented on June 24, 2024

Thank you for your prompt reply, it has resolved a significant issue for me. However, I still have another question. If I don't want to compare the GT column, meaning I currently don't have a phased VCF file, are there any appropriate parameters I can use to address this issue? I haven't found a suitable solution yet.

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ACEnglish avatar ACEnglish commented on June 24, 2024

truvari bench does not require phased genotypes. By default the genotypes are not used to prevent variants from matching and each variant is allowed to match to a single most-similar counterpart with --pick single. Each variant can participate in as many 1-to-1 matches with --pick multi. Allele counts from the genotypes are used with --pick ac. See wiki for details.

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xiaomiyongyuan avatar xiaomiyongyuan commented on June 24, 2024

Thank you so much for your answer !

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