Question: Varscan Filtering scripts: very little overlap between output of varscan filtering scripts
gravatar for Chirag Nepal
5.0 years ago by
Chirag Nepal2.2k
Chirag Nepal2.2k wrote:

Hi There,

I am using varscan2 (for matched N/T pairs) to call somatic SNVs. For filtering, i used script from varscan to filter high confidence somatic call.  I used two scripts from varscan, and i get completely different results with very little overlap.


Filter script-1

java -jar VarScan.v2.3.7.jar processSomatic $name

This will be two output files, namely $name.Somatic and $name.Somatic.hc (high confidence output )


Filter script-2

java -jar VarScan.jar somaticFilter $name.Somatic --min-coverage 15 --min-reads2 5 --min-strands2 2 --p-value 0.001 --output-file $name.Somatic.hc"Criteria2"


Overlap between two high-confidence somatic calls,

overlap is about 10%. Why two filtering criteria are so discordant.

Any insight will be helpful.







filter-varscan snv varscan exome • 2.1k views
ADD COMMENTlink written 5.0 years ago by Chirag Nepal2.2k
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