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

rcholicrcholic DenverMember Posts: 68

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?

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