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Old 04-28-2014, 11:58 AM   #1
persorrels
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Location: San Jose, CA

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Default 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?
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Old 04-29-2014, 07:23 AM   #2
KaiYe
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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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