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-   -   Filter somatic calls in Pindel output (http://seqanswers.com/forums/showthread.php?t=42881)

persorrels 04-28-2014 11:58 AM

Filter somatic calls in Pindel output
 
I'm running Pindel on some normal/tumor pairs. A lot of calls seem to be germline. Is there a filtering script out there to get the somatic calls?

KaiYe 04-29-2014 07:23 AM

You could do an awk selection based on the number of samples and the numbers of reads supporting the ALT. then filtering dbSNP entries and restrict homopolymer and micro satellite calls to regions called somatic by MSIsensor.


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