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?


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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