Filtering out SNPs based on Genotype Quality (GQ)

[MurielGB]

Hello,

I used GATK to call variants.

I want to filter the vcf file based on genotype quality.
If a genotype has a GQ<20, I would like the corresponding genotype to be replaced by missing data (./.).

I used GATK to filter :

java  -Xmx20g -jar GenomeAnalysisTK.jar \
	-T VariantFiltration \
	-R ../ref.fasta \
	-V vcf_snp_f1.vcf \
	-o vcf_snp_f11.vcf \
	--genotypeFilterExpression "GQ <= 20" \
	--genotypeFilterName "LowGQ" \

And I obtain a vcf where the genotypes fields look like that :
If GQ>20, then :

0/1:2,3:5:PASS:44:95,0,44

The "PASS" appears.

But if GQ<20, then :

0/0:2,0:2:LowGQ:6:0,6,68

It's written LowGQ.

The thing is that for almost all SNPs, I have a LowGQ in one or more individuals so I can't filter out the SNP using "grep -v LowGQ".

I would prefer the corresponding genotype to be replaced by "./." (missing).

Is there a tool to do that or I have to write a bash script ?

Thanks a lot for your help,

Muriel

[TiborNagy]

You need to write a script.

[Jeremy]

vcffilter from vcflib will replace with "./."