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Old 11-29-2011, 08:59 AM   #1
Location: Maryland

Join Date: Apr 2010
Posts: 31
Default BFAST and Variant Calling


I have a question regarding variant calling with SOLiD data. For the mapping, I used BFAST and for variant calling I'm trying to use GATK.

The problem occurs when I run the quality score recalibration and also the unified genotyper. Whenever I run these I get an output that says many of my reads were filtered because they don't have a mapping quality (The MappingQualityUnavailableFilter contains nearly 90% of my reads, also see here:

In other words the mapping quality was 255 which in a sam/bam file means the quality is unavailable.

Here ( it seems the mapping quality of 255 is actually very good.

I'm confused as to how to work around this problem. Any help would be appreciated. Thanks.
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