vcf-fix-ploidy(1) 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 },
],
}