| VCF-FIX-PLOIDY(1) | User Commands | VCF-FIX-PLOIDY(1) |
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 },
- ],
- }
| February 2013 | vcf-fix-ploidy |