Question: Deletions
gravatar for Laura Reinholdt
7.2 years ago by
Laura Reinholdt20 wrote:
I have a DNA seq data set from mouse genome that is heterozygous for a known 15 bp deletion. The deletion is listed in the SAM tools pileup: mapping quality = 690, SNP quality =690, mapping quality =52, coverage = 62, 11 reads span the deletion, 52 reads are reference. When I use SAM tools ‘filter pileup on coverage and SNPs’, this deletion is filtered out. I’m using the default settings for the filter: coverage=3, quality cap=60 (is this the Phred quality score or is it the Phred quality coefficient?). Does anyone whether this deletion is filtered out simply because it’s a deletion or is it filtered out due to the mapping quality? Can anyone suggest an alternative tool / setting for filtering the pileup? Thanks, Laura Laura Reinholdt, PhD Research Scientist Genetic Resource Sciences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609-1500 (207) 288-6000, ext. 6693
snp • 815 views
ADD COMMENTlink modified 7.2 years ago by Jennifer Hillman Jackson25k • written 7.2 years ago by Laura Reinholdt20
gravatar for Jennifer Hillman Jackson
7.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Laura, The tool's form does not have an upper quality threshold, but rather a minimum quality score value ("Do not consider read bases with quality lower than:" this is defaulted to 20). The value is a Phred 33 score. If you had the minimum quality threshold set to 60, then yes, this could certainly have removed sequences from the region. Set this value to the default or to another value determined by evaluating the range of base qualities in your data. Use tools "NGS: QC and manipulation" -> 'Compute quality statistics' and 'Build base quality distribution'. Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.2 years ago by Jennifer Hillman Jackson25k
For you and other following this thread, there is one extra tool that can be recommended for quickly evaluating datasets: "NGS: QC and manipulation -> FastQC". In many cases, this can replace the other quality score evaluation tools. Take care, Jen -- Jennifer Jackson
ADD REPLYlink written 7.2 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour