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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	%INFO/NOVELTY	%INFO/NOVELAL	%INFO/NOVELGT[	%SAMPLE %GTR
              %PL]
'

              #  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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