VCF-FIX-PLOIDY(1)

📦 version 0.1.17, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 vcf-fix-ploidy(1) 💖

okay bestie, welcome to the User Commands corner of the manual, where we fix up your ploidy situation and make your VCF actually make sense. no cap, this one's a little legend. 🦋

✨ NAME ✨

vcf-fix-ploidy — literally just vcf-fix-ploidy, she's her own name, main character energy from day one 👑

🌈 SYNOPSIS 🌈

cat broken.vcf | vcf-fix-ploidy [OPTIONS] > fixed.vcf

pipe your sad little broken file in, get a fixed one out. iconic behaviour. 💅

🎀 OPTIONS 🎀

  • -a, --assumed-sex <sex> — M or F. this one is required if the list you gave with -s isn't complete, so don't skip it and then act surprised 🙈
  • -l, --fix-likelihoods — adds or removes het likelihoods. heads up bestie, this is not the default behaviour, it's opt-in only ✨
  • -p, --ploidy <file> — the ploidy definition file. the default one is shown down below, don't worry, she's right there 🫶
  • -s, --samples <file> — a list of sample sexes, formatted like sample_name [MF] 🍓
  • -h, -?, --help — this help message. hi, that's me, the help message 💖

🌸 Default ploidy definition 🌸

here's the default, in all her glory, verbatim, no edits, because we respect the source material 💜

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 },
],
}

and that's the whole page, bestie, you ate it. 💅✨

vcf-fix-ploidy — February 2013 — that's the version and the date, periodt, see you in the next manpage 🎀💖

📦 where this page comes from