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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
    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?
    Attached Files
    Last edited by elfuser; 07-31-2012, 12:02 PM.

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