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Old 06-28-2013, 12:56 PM   #2
dkoboldt
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Location: St. Louis

Join Date: Mar 2009
Posts: 62
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Elena,

You could probably just perform steps 1 and 3 and get a good high-confidence set of somatic mutation calls.... the somaticFilter command is more simplistic than the filter false positives.

If you want the germline calls, combine Germline.hc and LOH.hc files, and then run that through the false positive filter with the NORMAL bam.

As for bam-readcount, I'd recommend at least mapping quality of 1 and base quality of 15.
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