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
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