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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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how to output wildtype site via VarScan with SNP calling ? #14

Closed WinterLi1993 closed 8 years ago

WinterLi1993 commented 8 years ago

HI, I wanna use VarScan to produce calls at variant sites and confident reference sites, but I can not find any parameters .

dkoboldt commented 8 years ago

Hello, you can do this using the VarScan "mpileup2cns" command. However, it only works if you don't provide the "--variants" or "--output-vcf" parameters, as both of these force variant-position-only reporting.

Incidentally, for VarScan somatic, the --validation 1 parameter will force it to output wild-type calls with good coverage.