When my reads quality and alignment is good, why the VCF files contains ./. (not detected?) info?

rcholicrcholic DenverPosts: 68Member

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?



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,434Administrator, GATK Dev admin

    Normally the only reason GATK would output ./. is if the site had no usable coverage. You may want to run DiagnoseTargets to find which intervals are problematic.

    Geraldine Van der Auwera, PhD

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