Category

Genome Variant Analysis


Usage

java -jar VarScan.jar somaticFilter [mutations file] OPTIONS


Manual

--min-coverage  Minimum read depth [10]
--min-reads2    Minimum supporting reads for a variant [2]
--min-strands2  Minimum # of strands on which variant observed (1 or 2) [1]
--min-avg-qual  Minimum average base quality for variant-supporting reads [20]
--min-var-freq  Minimum variant allele frequency threshold [0.20]
--p-value       Default p-value threshold for calling variants [1e-01]
--indel-file    File of indels for filtering nearby SNPs
--output-file   Optional output file for filtered variants


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