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Genotyping known variants with GenotypeGVCFs

gmagoongmagoon Member
edited February 2018 in Ask the GATK team

Hi Geraldine, Sheila, and others,
Now that it seems that a fix for the "GGA" feature in HaplotypeCaller may be forthcoming in some future GATK release has been made in a recent GATK 4 release, I was wondering about the prospects for a GENOTYPE_GIVEN_ALLELES mode for GenotypeGVCFs. There understandably seems to be a significant amount of interest in this sort of capability, e.g. here, and here.

To be more concrete, I'm thinking about something that would function like the following example:
Given the following as known variants of interest, specified in an -alleles option:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
20  10000694    .   G   A   .   .   .
20  10001661    .   T   C   .   .   .

...GenotypeGVCFs would take an input gVCF, like the simplified single-sample example below:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Sample1
20  10000694    .   G   T,<NON_REF> .   .   .   GT:DP:GQ    0/1:29:99
20  10000695    .   G   <NON_REF>   .   .   END=10001999    GT:DP:GQ    0/0:0:0

...and produce something like the following as output:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Sample1
20  10000694    .   G   A,<NON_REF> .   .   .   GT  0/2
20  10001661    .   T   C,<NON_REF> .   .   .   GT  ./.

With GATK 3, I believe there was a partial solution involving use of -allSites -L sites.vcf, but from the current GenotypeGVCFs source code, it looks like the -allSites option is now ignored and unsupported (and is also omitted from the GATK 4 docs).

Should I be writing my own tools to genotype known variants from the gVCFs, or is this something where we might expect an official GenotypeGVCFs feature in the not-too-distant future? Or maybe there is some straightforward way of doing this currently (aside from using UnifiedGenotyper or HaplotypeCaller with BAM file input and GENOTYPE_GIVEN_ALLELES) that I have overlooked?

Thanks very much in advance,
Greg

Post edited by gmagoon on

Best Answer

Answers

  • gmagoongmagoon Member

    Thanks very much, Sheila.

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