Man page - vcf-contrast(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-CONTRAST

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Example:

---

NAME

vcf-contrast - finds differences amongst samples

SYNOPSIS

vcf-contrast +<list> -<list> [ OPTIONS ] file.vcf.gz

DESCRIPTION

About: Finds differences amongst samples adding NOVEL* annotation to INFO field.

OPTIONS

+<list>

List of samples where unique variant is expected

-<list>

List of background samples

-d , --min-DP <int>

Minimum depth across all -<list> samples

-f , --apply-filters

Skip sites with FILTER column different from PASS or "."

-n , --novel-sites

Print only records with novel genotypes

-h , -?, --help

This help message.

Example:

# Test if any of the samples A,B is different from all C,D,E vcf-contrast +A,B -C ,D,E -m file.vcf.gz

# Same as above but printing only sites with novel variants and table output vcf-contrast -n +A,B -C ,D,E -m file.vcf.gz | vcf-query -f ’%CHROM %POS\t%INFO/NOVELTY\t%INFO/NOVELAL\t%INFO/NOVELGT[\t%SAMPLE %GTR %PL]\n’

# Similar to above but require minimum mapping quality of 20 vcf-annotate -f MinMQ=20 file.vcf.gz | vcf-contrast +A,B,C -D ,E,F -f

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