The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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