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6.0 years ago
fabbri.marco
▴
10
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