Provided by: vcftools_0.1.11+dfsg-1_amd64
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