Provided by: vcftools_0.1.11+dfsg-1_amd64
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