NAME

       vcf-fix-ploidy - vcf-fix-ploidy

SYNOPSIS

       cat broken.vcf | vcf-fix-ploidy [OPTIONS] > fixed.vcf

OPTIONS

       -a, --assumed-sex <sex>
              M or F, required if the list is not complete in -s

       -l, --fix-likelihoods
              Add or remove het likelihoods (not the default behaviour)

       -p, --ploidy <file>
              Ploidy definition. The default is shown below.

       -s, --samples <file>
              List of sample sexes (sample_name [MF]).

       -h, -?, --help
              This help message.

   Default ploidy definition:
              ploidy => {

              X => [

              #  The  pseudoautosomal  regions  60,001-2,699,520 and 154,931,044-155,270,560 with the ploidy 2 {
              from=>1, to=>60_000, M=>1 }, { from=>2_699_521, to=>154_931_043, M=>1 },

              ], Y => [

              # No chrY in females and one copy in males { from=>1, to=>59_373_566, M=>1, F=>0 },

              ], MT => [

              # Haploid MT in males and females { from=>1, to => 16_569, M=>1, F=>1 },

              ],

              }

vcf-fix-ploidy                                    February 2013                                VCF-FIX-PLOIDY(1)