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 FILTER,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