VariantFiltration and SelectVariants
Posted in Ask the team | Last updated on 2013-01-07 20:12:46


Comments (6)

I am trying to filter variant calls which have "GQ>=20.0".

GATK SelectVariants, gives no error but gives only the header in the output file

java -Xmx2g -jar ~/GenomeAnalysisTKLite-2.1-8-gbb7f038/GenomeAnalysisTKLite.jar -R xxx -T SelectVariants --variant xxx.var.flt.vcf -o xxx.vcf -select "GQ >= 20.0"

So, I tried using VariantFiltration followed by SelectVariants. The variant filtration seems to work fine adding FT tag to the format field. And then I am trying to get records having FT tag using the following commands

java -Xmx2g -jar ~/GenomeAnalysisTKLite-2.1-8-gbb7f038/GenomeAnalysisTKLite.jar -R xxx -T VariantFiltration --variant xxx.var.flt.vcf -o xxx_filtered.vcf --genotypeFilterExpression "GQ >= 20.0" --genotypeFilterName "qual_1_filters"

java -Xmx4g -jar ~/GenomeAnalysisTKLite-2.1-8-gbb7f038/GenomeAnalysisTKLite.jar -T SelectVariants -R xxx --variant xxx_filtered.vcf -select 'vc.hasAttribute("FT")' -o xxx_qual20.vcf 

but I only get header in the output vcf file.

I am not sure if this is the right approach. Any help would be appreciated.


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