VcfGenomeStat
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vcfGenomeStat - print flanking sequences and how often they appear for input vcf file.
Usage
../bin/vcfGenomeStat [-L <integer>] [-w <integer>] [-l <string>] -o <string> -i <string> -r <string> [-v] [--] [--version] [-h] Where: -L <integer>, --max-line-length <integer> Maximun Line Length of the VCF file (default:1048576) -w <integer>, --win <integer> Window size for HomPolymerRun (default:10) -l <string>, --log <string> Log file - [out].log is default -o <string>, --out <string> (required) Output file -i <string>, --in <string> (required) Input VCF file -r <string>, --reference <string> (required) Karma's reference sequence -v, --verbose Turn on verbose mode --, --ignore_rest Ignores the rest of the labeled arguments following this flag. --version Displays version information and exits. -h, --help Displays usage information and exits.