This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Number of KEEP vs. REJECT calls
I'm wondering what people are seeing in terms of the number of keep vs. reject calls in a typical Illumina exome sequencing tumor/normal pair. Briefly, I'm using a BFAST for aligning followed by the general GATK steps for clean-up; the data looks clean with no quality control issues. MuTect (with dbsnp and cosmic for hg19) and the default parameters (high confidence mode, without panel of normals) generally returns a total of ~600K mutations; on average, only 100 of these are marked as keep! I would expect this number to be higher. I'm currently re-running MuTect with the extended output turned on to see the detailed rejection criteria, but is there anything specific (i.e. obvious that I am missing) that I should look closely at first to make sure that there is not a technical or processing error? I'm also setting up running orthogonal analyses with somaticsniper and jointsnvmix for comparison. Thanks!