Man page - vcf-stats(1)
Packages contas this manual
- vcf-subset(1)
- vcf-merge(1)
- vcf-compare(1)
- vcf-to-tab(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-contrast(1)
- vcf-isec(1)
- vcf-validator(1)
- fill-ref-md5(1)
- vcf-convert(1)
- vcf-annotate(1)
- vcf-concat(1)
- fill-an-ac(1)
- vcf-fix-newlines(1)
- vcf-query(1)
- vcf-stats(1)
- vcf-consensus(1)
- vcf-tstv(1)
- fill-aa(1)
- vcf-phased-join(1)
- fill-fs(1)
- vcf-shuffle-cols(1)
- vcftools(1)
- vcf-fix-ploidy(1)
Package: vcftools
apt-get install vcftools
apt-get install vcftools
Manuals in package:
Documentations in package:
Manual
| VCF-STATS(1) | User Commands | VCF-STATS(1) |
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
| July 2011 | vcf-stats 0.1.5 |