Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

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

rcholicrcholic DenverPosts: 63Member

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.