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bbmap callvariants.sh multisample vcf format, wrong number of fields

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  • bbmap callvariants.sh multisample vcf format, wrong number of fields

    Trying to use BBMap callvariants on multiple samples. The resulting VCF does not have the sample names and yields an error with any vcf tools:

    Code:
    vcf-validator tmp.vcf 
    Wrong number of fieldsin tmp.vcf; expected 15, got 16. The offending line was: [... the first line of variants]
    The VCF:
    Code:
    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  FORMAT  FORMAT  FORMAT  FORMAT  FORMAT  FORMAT
    BBMap command:
    Code:
    callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa 
    #ive also tried using the output command, no change
    callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa vcf0=S1,S2,S3,S4,S5,S5
    #As well as each sample using the "in" command
    callvariants.sh multisample=t in=S1.sam,S2.sam,S3.sam,S4.sam,S5.sam,S6.sam out=tmp.vcf ref=genome.fa overwrite=t vcf0=AO,GG,OG,SF,TH,Tum
    I think BBMap could be a very powerful set of tools and I am expecting I am missing something pretty basic!

  • #2
    Hi Greg,

    Sorry about that, there was a bug that slipped in around v37.87 with regards to multisample VCF names. It's fixed in v37.96 which I will release this week.

    -Brian

    Comment


    • #3
      Okay cool, thanks for the quick response!

      Comment


      • #4
        Same error here: downloaded BBMap 2 weeks ago, finishing my snp calling pipeline today, same problem and discovering the patch went out 10 days ago...

        Thx for the fix

        Comment


        • #5
          Oh, yep - it's fixed now, sorry for not mentioning that!

          Comment


          • #6
            I have another problem: when using vcf0=, followed by files locations separated by comma, callvariants.sh create subdirectory instead of just creating files at specified location.

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