Identify Variant Callers Supported Per Consensus SNV

[zhuchcn]

How to tell which variant callers were each consensus SNV called?

In this bcftools sites file below, the last column is a binary string, which I assume indicates the variant callers that supports each record? If yes, how should I interpret it?

/hot/project/process/MissingPeptides/MISP-000132-MissingPeptidesPanCanP1/CPTAC_PAAD/WXS/metapipeline-DNA-6.0.0-rc.4/CPTAC_PAAD/main_workflow/output/call-sSNV-8.1.0/C3L-00017-02/Intersect-BCFtools-1.17/output/isec-2-or-more/BCFtools-1.17_CPTAC-PAAD_C3L-00017-02_sites.txt

chr1   2629382    G  C  0101
chr1   3730955    C  T  1101
chr1   31683232   G  A  1111
chr1   54781419   G  A  1111
chr1   158766565  A  T  1101
chr1   160084738  C  T  1101
chr1   160881972  C  T  1111
chr1   177061117  C  T  1111
chr1   225850043  C  T  1101
chr1   240092440  G  A  1111

This is from the vcftools README.txt:

This file was produced by vcfisec.
The command line was:   bcftools isec  --nfiles +2 --output-type z --prefix isec-2-or-more --regions-file nexterarapidcapture_exome_targetedregions_v1.2_GRCh38.bed.gz MuSE-2.0.4_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz Mutect2-4.5.0.0_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz SomaticSniper-1.0.5.0_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz Strelka2-2.9.10_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz

Using the following file names:
isec-2-or-more/0000.vcf.gz      for stripped    MuSE-2.0.4_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz
isec-2-or-more/0001.vcf.gz      for stripped    Mutect2-4.5.0.0_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz
isec-2-or-more/0002.vcf.gz      for stripped    SomaticSniper-1.0.5.0_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz
isec-2-or-more/0003.vcf.gz      for stripped    Strelka2-2.9.10_CPTAC-PAAD_C3L-00017-02_SNV-reorder.vcf.gz

So does 0101 mean the first record is supported by Mutect2 and Strelka2 but not MuSE and SomaticSniper?

[yashpatel6]

That should be the correct interpretation, @sorelfitzgibbon to confirm

[sorelfitzgibbon]

Sorry I didn't see this earlier. Yes, that is correct. If you're also interested in private variants you should use isec-1-or-more.

[zhuchcn]

Thanks for confirming. Worth adding some kind of documentation? If the information can be added to the README.txt or the site.txt that will be very helpful.