VQSR on sex chromosomes only
I have a WES variant calling project for hundreds of patients, and the last run of calling used GATK v3.1 quite some time ago. Now I want to use v3.4 to redo the variant calling on sex chromosomes only and compare the variants in sex chromosomes between case and control groups. Here is my plan and I wonder if it's OK to do the VQSR on sex chromosomes only?
HaplotypeCaller -i boy.bam -ploidy 1 -L X,Y -o boy_XY.g.vcf HaplotypeCaller -i girl.bam -L X -o girl_X.g.vcf CombineGVCFs -v boys.XY.gvcf.list -o boys.XY.g.vcf CombineGVCFs -v girls.X.gvcf.list -o girls.X.g.vcf GenotypeGVCFs -v boys.XY.g.vcf -v girls.X.g.vcf -o all.XY.vcf