Man page - vcf-stats(1)

Packages contains this manual

Package:  vcftools
apt-get install vcftools

Manuals in package:
• vcf-query(1)
• vcf-stats(1)
• vcf-to-tab(1)
• vcf-concat(1)
• vcf-sort(1)
• vcf-indel-stats(1)
• vcf-phased-join(1)
• fill-aa(1)
• vcf-isec(1)
• vcf-consensus(1)
• vcf-tstv(1)
• vcf-merge(1)
• vcf-subset(1)
• vcf-contrast(1)
• vcf-fix-newlines(1)
• fill-an-ac(1)
• vcftools(1)
• vcf-validator(1)
• fill-fs(1)
• vcf-fix-ploidy(1)
• vcf-compare(1)
• fill-ref-md5(1)
• vcf-annotate(1)
• vcf-convert(1)
• vcf-shuffle-cols(1)
Documentations in package:
• vcftools

Manual

VCF-STATS

NAME
SYNOPSIS
OPTIONS
EXAMPLES

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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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