Questions about GenotypeVCFs output
I generated 12 .g.vcf files with HaplotypeCaller in GVCF mode and then a vcf with GenotypeGVCFs. What's the easiest way to split this vcf per sample ? Should I apply hard filtering first and then split the vcf per sample ? (These vcf are normal exomes, I would like to use them afterwards with Mutect2).
Moreover, lines of the vcf file are annotated differently : BaseQRankSum, ClippingRankSum, ExcessHet, MQRankSum, ReadPosRankSum appear at some lines but not all of them (I get the same when I create a vcf with HaplotypeCaller without GVCF mode). Do you know why ? Is it possible to change this ? Will it be a problem at the hard filtering step when I'll handle variants with SelectVariants, and VariantFiltration ?
Thanks a lot!