vcf-stats(1) statistic of VCF file


vcf-stats [OPTIONS] file.vcf.gz


-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.


# 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