This is the command vcf-stats that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use vcf-stats online using onworks.net services
