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Mutect2 files from TCGA - FORMAT tag [QSS] expected different number of values (expected 1, found 2)

Hi,

I am trying to run vcf-validator (vcftools) on some VCF files I obtained from TCGA. These files are tumor-normal vcf files called using Mutect2. When I try and run vcf validator I get an error:

------------------------
Summary:
6220 errors total

6220 .. column NORMAL at chr1:14677 .. FORMAT tag [QSS] expected different number of values (expected 1, found 2)


Any ideas on what is wrong and what I can do to fix it?

Thanks
Tagged:

Answers

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @alcam1 Any Mutect2 vcf with the QSS annotation is from a very old, unsupported version. More recent releases produce valid VCFs.

  • alcam1alcam1 Member
    > @davidben said:
    > @alcam1 Any Mutect2 vcf with the QSS annotation is from a very old, unsupported version. More recent releases produce valid VCFs.

    Ok thank you. The VCF files I have were directly downloaded from TCGA though, is there any way around this apart from getting the BAM files and calling the variants again?
  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    Hmmm, is there a VCF header line for QSS that says it has one value? If so maybe switching the "1" to a "2" would work.

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