vcf-fix-ploidy (1)

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

-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 },

• ],

• }