Hi,
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: http://www.broadinstitute.org/gsa/wi...TK_release_1.1).
In other words the mapping quality was 255 which in a sam/bam file means the quality is unavailable.
Here (http://sourceforge.net/apps/mediawik...apping_Quality) 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.
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: http://www.broadinstitute.org/gsa/wi...TK_release_1.1).
In other words the mapping quality was 255 which in a sam/bam file means the quality is unavailable.
Here (http://sourceforge.net/apps/mediawik...apping_Quality) 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.
Comment