vcf-fix-ploidy1
Vcf-fix-ploidy
Usage
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 },
-
],
-
}
Releases
Unchanged in 6 releases since Debian 8 (Jessie).