ALLELECOUNTER(1p)

💖 NAME 💖

alleleCounts.pl — bestie, this one makes you a tab-separated file with allelic counts and depth for every locus you point it at. Every. Single. One. 🧬✨

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✨ SYNOPSIS ✨

Okay so real talk first: if your data is large, use the C version where you can, because it's also more configurable. Like, she's the upgrade. 👑

alleleCounts.pl

🫶 Required (no skips, these are the bare minimum)

• -bam, -b — your BAM/CRAM file. She expects a co-located index, so have that ready. If it's a CRAM, go look at -ref below. 💅
• -output, -o — the output file. Defaults to [STDOUT] if you don't say anything.
• -loci, -l — the alternate loci file. It literally just needs chr and pos. But heads up: the output is different for this one — you get counts for each residue. 🙈

🌸 Optional (mix and match, go off)

• -ref, -r — genome.fa. Required for CRAM, and it needs a colocated .fai next to it.
• -minqual, -m — minimum base quality to include (integer). Default is [30].
• -mapqual, -q — minimum mapping quality of a read (integer). Default is [35].
• -gender, -g — a flag. Its presence means your loci file gets treated as gender SNPs. 🎀 Cannot be used with s.
• -snp6, -s — a flag. Its presence means your loci file is in SNP6 format. 🎀 Cannot be used with g. Also it changes the output format, so don't be surprised.
• -help, -h — this message. Hiiii. 👋
• -version, -v — the version number.

Not me stressing the g / s thing: those two flags are mutually exclusive, periodt. Pick one. 💀

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perl v5.40.0 🦋 2024-12-10 — that's the tea, bestie, that's when this page was living its moment. Stay iconic, run your counts, and hydrate. 💜🌈⭐