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--min-freq-for-hom in VarScan #1

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billzt opened this issue Oct 8, 2017 · 0 comments

billzt commented Oct 8, 2017

https://github.com/OpenGene/ctdna-pipeline/blob/master/pipeline.sh#L24 says:

java -jar VarScan.v2.3.8.jar mpileup2snp outdir/test.dedup.mpileup --min-coverage 4 --min-reads2 2 --min-avg-qual 20 --min-var-freq 0.001 --min-freq-for-hom 90 --output-vcf 1 >outdir/test.snp.vcf

Now I'm not sure whether the value of --min-freq-for-hom 90 is OK. Because now the new version of VarScan (v2.4.3) says:

USAGE: java -jar VarScan.jar mpileup2cns [pileup file] OPTIONS
        mpileup file - The SAMtools mpileup file

        OPTIONS:
...
        --min-freq-for-hom      Minimum frequency to call homozygote [0.75]
...

Note, the default value is 0.75 rather than 75 (%). Therefore perhaps we should use value 0.9 rather than 90 (5)

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