varscan not taking opstions

Question

[fabbri.marco]

I am running varscan 2.4.3, mpileup2snp is not taking the settings as you can below, it works but with default settings any suggestion how to change them?

varscan mpileup2snp  sam1 –-min-coverage 10 –-min-var-freq 0.05 –-p-value 0.05 --output-vcf 1 > test6var005.vcf
Only SNPs will be reported
Warning: No p-value threshold provided, so p-values will not be calculated
Min coverage:   8
Min reads2: 2
Min var freq:   0.2
Min avg qual:   15
P-value thresh: 0.01
Reading input from sam1

thanks

Marco

Answer 1

[Pierre Lindenbaum]

varscan is a java program. It must be invoked with something like:

USAGE: java -jar VarScan.jar  [COMMAND] [OPTIONS]

I imagine, you're using a bash wrapper around the command above. Don't use this wrapper and invoke varscan directly with java.