Question: Snp Quality Distribution Peaks At 222 From Variant Call Pile
0
gravatar for Juliofdiaz
7.8 years ago by
Juliofdiaz130
Toronto, Ontario, Canada
Juliofdiaz130 wrote:

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?

samtools bwa • 1.8k views
ADD COMMENTlink modified 5.0 years ago by swbarnes27.8k • written 7.8 years ago by Juliofdiaz130
1
gravatar for swbarnes2
5.0 years ago by
swbarnes27.8k
United States
swbarnes27.8k wrote:

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

ADD COMMENTlink written 5.0 years ago by swbarnes27.8k
0
gravatar for Marand
5.0 years ago by
Marand0
United States
Marand0 wrote:

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). 

ADD COMMENTlink written 5.0 years ago by Marand0

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

ADD REPLYlink written 5.0 years ago by Marand0
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