Effect of LeftAlignAndTrimVariants with --splitMultiallelics tool

How does the LeftAlignAndTrimVariants with --splitMultiallelics tool affects the AC, AF, AN fields and also if multiple alleles are split then on what basis it splits the PL field which helps to determine the genotype.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rutujagtap08
    Hi,

    All the fields should be split by allele, unless you request --keepOriginalAC. Can you post an example record you are asking about?

    Thanks,
    Sheila

  • rutujagtap08rutujagtap08 PuneMember

    HI

    Here is one example. I have used LeftAlignAndTrimVariants with --splitMultiallelics, now how does GATK determines in PL value and decides the genotype for second allele ?

    Original File
    chrI 409 . G A,T 98 . DP=31;VDB=5.556450e-02;AF1=1;AC1=2;DP4=0,0,29,2;MQ=20;FQ=-105 GT:PL:GQ 1/1:131,78,0,111,6,95:99
    LeftAlignAndTrimVariants with --splitMultiallelics tool
    chrI 409 . G A 98 . AC=2;AF=1.00;AN=2; GT:GQ:PL 1/1:99:131,78,0
    chrI 409 . G T 98 . AC=0;AF=0.00;AN=2; GT:GQ:PL 0/0:99:36,16,0

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rutujagtap08
    Hi,

    Interesting. That is unexpected. Is that the entire record for the site before splitting? How did you produce the VCF? Are you using the latest version of GATK?

    Thanks,
    Sheila

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