This is the command vcf-fix-ploidy that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 },
],
}
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