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!