Usage: pv vardict single filter [OPTIONS]
This tool helps to filter vardict version 1.4.6 VCFs for single sample
calling
Options:
-i, --inputVcf FILE Input vcf generated by vardict which needs
to be processed [required]
--tsampleName TEXT Name of the tumor Sample [required]
-dp, --totalDepth INTEGER RANGE
Tumor total depth threshold [default: 20;
x>=20]
-ad, --alleledepth INTEGER RANGE
[x>=1]
-tnr, --tnRatio INTEGER Tumor-Normal variant fraction ratio
threshold [default: 1]
-vf, --variantFraction FLOAT Tumor variant fraction threshold [default:
5e-05]
-mq, --minQual INTEGER Minimum variant call quality [default: 0]
-fg, --filterGermline Whether to remove calls without 'somatic'
status
-o, --outDir TEXT Full Path to the output dir
--help Show this message and exit.