vcf-stats(1) debian man page | unix.com

VCF-STATS(1)							   User Commands						      VCF-STATS(1)

NAME
       vcf-stats - statistic of VCF file

SYNOPSIS
       vcf-stats [OPTIONS] file.vcf.gz

OPTIONS
       -d, --dump <file>
	      Take an existing dump file and recreate the files (works with -p)

       -f, --filters <filter1,filter2>
	      List of filters such as column/field (any value), column/field=bin:max (cluster in bins),column/field=value (exact value)

       -p, --prefix <dir/string>
	      Prefix of output files. If slashes are present, directories will be created.

       -s, --samples <list>
	      Process only the listed samples, - for none. Excluding unwanted samples may increase performance considerably.

       -h, -?, --help
	      This help message.

EXAMPLES
	      #    Calculate   stats   separately   for   the	filter	 field,   quality   and   non-indels   vcf-stats   file.vcf.gz	 -f   FIL-
	      TER,QUAL=10:200,INFO/INDEL=False -p out/

	      # Calculate stats for all samples vcf-stats file.vcf.gz -f FORMAT/DP=10:200 -p out/

	      # Calculate stats only for the sample NA00001 vcf-stats file.vcf.gz -f SAMPLE/NA00001/DP=1:200 -p out/

	      vcf-stats file.vcf.gz > perl.dump

vcf-stats 0.1.5 						     July 2011							      VCF-STATS(1)