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07-31-2012, 11:42 AM
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Member
Location: Toronto, ON Join Date: Dec 2009
Posts: 16
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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 Code:
'($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' Last edited by elfuser; 07-31-2012 at 12:02 PM. |
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