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