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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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Suggestions for using Varscan2 on tumor only samples ? #39

Open kmavrommatis opened 5 years ago

kmavrommatis commented 5 years ago

Are there any recommendations on how to run varscan2 to find mutations on tumor only samples (i.e. without a matched normal available). Would running it in 'germline' mode, but allowing more flexible thresholds be sufficient ? Would applying filters like processSomatic (or somaticFilter) make sense? Any other suggestions? Thanks in advance

LeilyR commented 2 years ago

did you get an answer for that?