Man page - vcf-fix-ploidy(1)
Packages contains this manual
- vcf-query(1)
- vcf-stats(1)
- vcf-to-tab(1)
- vcf-concat(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-phased-join(1)
- fill-aa(1)
- vcf-isec(1)
- vcf-consensus(1)
- vcf-tstv(1)
- vcf-merge(1)
- vcf-subset(1)
- vcf-contrast(1)
- vcf-fix-newlines(1)
- fill-an-ac(1)
- vcftools(1)
- vcf-validator(1)
- fill-fs(1)
- vcf-fix-ploidy(1)
- vcf-compare(1)
- fill-ref-md5(1)
- vcf-annotate(1)
- vcf-convert(1)
- vcf-shuffle-cols(1)
apt-get install vcftools
Manual
VCF-FIX-PLOIDY
NAMESYNOPSIS
OPTIONS
Default ploidy definition:
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 },
],
}