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Old 07-31-2012, 12:42 PM   #1
elfuser
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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:
vcfutils.pl varFilter -D30
and then filtered for low quality SNPs using awk
Code:
'($3=="*"&&$6>=50)||($3!="*"&&$6>=20)'
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?
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Last edited by elfuser; 07-31-2012 at 01:02 PM.
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