View Single Post
Old 07-31-2012, 12:42 PM   #1
Location: Toronto, ON

Join Date: Dec 2009
Posts: 16
Default SNP quality distribution peaks at 222 from variant call pile

I have reference mapped paired end illumina reads and called variants using BWA and Samtools respectively. The resulting vcf was treated to remove high coverage SNPs with
Code: varFilter -D30
and then filtered for low quality SNPs using awk
I graphed the distribution of SNP quality and observed a huge peak at 222., I repeated it with other samples and observed the same peak. Any clues as to why I may be seeing this?
Attached Images
File Type: png Picture1.png (22.4 KB, 10 views)

Last edited by elfuser; 07-31-2012 at 01:02 PM.
elfuser is offline   Reply With Quote