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

On 10/4/11 5:01 PM, Jennifer Jackson wrote:
Hello Laura,

On 10/3/11 11:05 AM, Laura Reinholdt 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

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.

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

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

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




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