Man page - vcf-contrast(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-CONTRAST(1) | User Commands | VCF-CONTRAST(1) |
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
| February 2013 | vcf-contrast |