ALLELECOUNTER(1)

🦋 ALLELECOUNTER(1) · User Commands 🦋

✨ NAME ✨

alleleCounter - NGS copy number algorithms 💅

🎀 SYNOPSIS 🎀

alleleCounter -l loci_file.txt -b sample.bam -o output.txt [-m int] [-r ref.fa.fai]

💖 DESCRIPTION 💖

Okay so this is support code for NGS copy number algorithms 🧬 You hand it a file of locations and a [cr|b]am file, and it gives you a count of coverage for each allele [ACGT] at every location, respecting whatever filter settings you picked ✨ It's giving precision, no cap.

🌸 OPTIONS 🌸

• -l, --loci-file [file] — Point it at your loci file. Main character energy 👑
• -b, --hts-file [file] — Path to your sample HTS file 🧚
• -o, --output-file [file] — Where the output file gets written 📝

Optional

• -r, --ref-file [file] — Path to the reference fasta index file 🗂️

Bestie, be careful! If CRAM format is supplied via -b and the reference listed in the CRAM header can't be found, alleleCounter may fail to work correctly 💀

• -m, --min-base-qual [int] — Minimum base quality. [Default: 20] 🫶
• -q, --min-map-qual [int] — Minimum mapping quality. [Default: 35] 🌈
• -c, --contig [string] — Limit calling to a named contig 🎯
• -d, --dense-snps — Lowkey a performance boost when lots of positions are packed close together 🚀
• -x, --is-10x — Turns on 10X processing mode 🌟 In this mode the HTS input file has to be a cellranger produced BAM file. Allele counts come out on a per-cellular barcode basis, with each count showing the consensus base for that UMI. Highkey iconic. Also, this mode works by iterating through bam file rather than using a 'fetch' approach 🔥
• -f, --required-flag [int] — Flag value of reads to keep when counting alleles. Default: [3] 🦋 N.B. if the proper-pair flag is selected, alleleCounter will assume paired-end and filter out any proper-pair flagged reads that aren't in F/R orientation 🙈
• -F, --filtered-flag [int] — Flag value of reads to exclude when counting alleles. Default: [3852] 🚫
• -v, --version — Shows the version number 🍓
• -h, --help — Shows the usage info 💜

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program 🌷

Bestie, that's the whole page 🫶 Version 4.1.0, dated May 2020, filed under ALLELECOUNTER(1) 💅✨