US Holiday notice: this Thursday and Friday (Nov 25-26) the forum will be unattended. Normal service will resume Monday Nov 29. Happy Thanksgiving!

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?

Tagged:

Answers

Sign In or Register to comment.