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Old 11-08-2013, 11:12 AM   #4
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Originally Posted by dkoboldt View Post

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.
Hi dkoboldt,

Can be used to filter the somatic indels?

Can I combine the indel vcf and snp vcf from the output of varscan somatic, and then filter the vcf file using step 1 and step 3? Does this works for both snp and indel in the vcf file?
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