(How to) Filter on genotype using VariantFiltration
Tutorials | Created 2018-07-03 | Last updated 2018-11-20

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Before using VariantFiltration, please read the entirety of the discussion in https://github.com/broadinstitute/gatk/issues/5362 that describes VariantFiltration's unintuitive behavior when processing compound expressions.

This tutorial illustrates how to filter on genotype, e.g. heterozygous genotype call. The steps apply to either single-sample or multi-sample callsets.

First, the genotype is annotated with a filter expression using VariantFiltration. Then, the filtered genotypes are made into no-call (./.) genotypes with SelectVariants so that downstream tools may discount them.

We use example variant record FORMAT fields from trio.vcf to illustrate.

0/1:17,15:32:99:399,0,439       0/1:11,12:23:99:291,0,292       1/1:0,30:30:90:948,90,0

1. Annotate genotypes using VariantFiltration

If we want to filter heterozygous genotypes, we use VariantFiltration's --genotype-filter-expression "isHet == 1" option. We can specify the annotation value for the tool to label the heterozygous genotypes with with the --genotype-filter-name option. Here, this parameter's value is set to "isHetFilter".

gatk VariantFiltration \
-V trio.vcf \
-O trio_VF.vcf \
--genotype-filter-expression "isHet == 1" \
--genotype-filter-name "isHetFilter"

After filtering, in the resulting trio_VF.vcf, our example record adds an FT field and becomes:

0/1:17,15:32:isHetFilter:99:399,0,439   0/1:11,12:23:isHetFilter:99:291,0,292   1/1:0,30:30:PASS:90:948,90,0

We see that HET (0/1) genotype calls get a isHetFilter in the FT field and other genotype calls get a PASS in the genotype field.

The VariantFiltration tool document lists the various options to filter on the FORMAT (aka genotype call) field:

We have put in convenience methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1"). Also available are expressions isCalled, isNoCall, isMixed, and isAvailable, in accordance with the methods of the Genotype object.

2. Transform filtered genotypes to no call

Running SelectVariants with --set-filtered-gt-to-nocall will further transform the flagged genotypes with a null genotype call. This conversion is necessary because downstream tools do not parse the FORMAT-level filter field.

gatk SelectVariants \
-V trio_VF.vcf \
--set-filtered-gt-to-nocall \
-O trioGGVCF_VF_SV.vcf

The result is that the GT genotypes of the isHetFiltered genotype records become null or no call (./.) as follows.

./.:17,15:32:isHetFilter:99:399,0,439   ./.:11,12:23:isHetFilter:99:291,0,292   1/1:0,30:30:PASS:90:948,90,0

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