Man page - vcf-fix-ploidy(1)
Packages contas this manual
- vcf-subset(1)
- vcf-merge(1)
- vcf-compare(1)
- vcf-to-tab(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-contrast(1)
- vcf-isec(1)
- vcf-validator(1)
- fill-ref-md5(1)
- vcf-convert(1)
- vcf-annotate(1)
- vcf-concat(1)
- fill-an-ac(1)
- vcf-fix-newlines(1)
- vcf-query(1)
- vcf-stats(1)
- vcf-consensus(1)
- vcf-tstv(1)
- fill-aa(1)
- vcf-phased-join(1)
- fill-fs(1)
- vcf-shuffle-cols(1)
- vcftools(1)
- vcf-fix-ploidy(1)
Package: vcftools
apt-get install vcftools
apt-get install vcftools
Manuals in package:
Documentations in package:
Manual
| 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 |