When my reads quality and alignment is good, why the VCF files contains ./. (not detected?) info?
My exome-seq reads quality is pretty good (120M reads) and the alignment using bwa is more than 95%. I use GATK to do the variant calling, however, the vcf output from VQSR contains many './.' fields, which I think means not detected?
I am wondering what's the possible cause for ./. ? my conditions are too stringent during gatk run?