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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 vcfutils.pl varFilter -D30, and then filtered for low quality SNPs using awk '($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?

bwa samtools
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updated by Ram Ram • written by Juliofdiaz Juliofdiaz

2 answers

If you do one sample at a time, 222 is the max quality allowable. So most of your called SNPs are of high quality.

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updated by Ram Ram • written by swbarnes2 swbarnes2

I am observing something similar in my own data. Has anyone figured this out? The rest of the distribution is normal except for this massive peak (QUAL=222).

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updated by Ram Ram • written by Marand • Marand

I should also mention that I filtered with vcfutils varFilter -d 5 -D 25... mapping and snp calling were executed with the same software as Juliofdiaz

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updated by Ram Ram • written by Marand • Marand

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