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Old 06-06-2013, 12:54 AM   #1
ElenaN
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Location: Moscow, Russia

Join Date: Nov 2012
Posts: 8
Default Filtering steps for VarScan2 somatic and germline calls

What is the proper filtering pipeline for somatic mutation detection using VarScan2, with tumor/normal paired samples?
My understanding of the steps:
0. VarScan2 somatic to make calls
Then filter:
1. VarScan2 processSomatic to separte calls Germline/Somatic/LOH and call some "high confidence"
2. VarScan2 somaticFilter on the Somatic.hc file to do further filtering.
- as I understand, this is where filtering for false positives aroudn indels take place
- it also seems to look at p-values and such - is it not redundant with the previous step?
3. fpfilter.pl on the resulting data for further filtering?
(in my hands this step seems to hang indefinitely without doing anything, though. not sure why)

My questions are:
- is this a correct order of steps, or are some of the 3 filtering steps redundant or obsolete?
- what are the recommended parameter settings for bam-read-count, especially mapping quality q? Should it be 1, as is recommended for mpileup, or higher?

Now, if I want to detect germline mutations in the same sample, can I just use the "Germline" (and I guess LOH) calls from VarScan?
Dan Koboldt seems to think so, as long as one uses the normal bamcount in step 3. Should "VarScan2 filter" be used in step 2? Or should a separate germline mutation caller be used for this purpose?

Thank you,
Elena
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