VcfGenomeStat
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Purpose
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.
