vcf-fix-ploidy - vcf-fix-ploidy
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.
- 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 },
- ],
- }