BAMCONSENSUS(1)

📦 version 2.0.185, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ bamconsensus — the manual, but make it cute ✨

okay bestie, welcome to BAMCONSENSUS(1) 💖 this is a General Commands Manual page, section 1, and it's genuinely one of my faves, no cap.

🌸 NAME 🌸

bamconsensus — compute a rough consensus sequence from alignments 🧬✨

🦋 SYNOPSIS 🦋

bamconsensus [reference=ref.fasta] < in.bam >out.fasta [options]

like... it reads from stdin and writes to stdout, she's a pipeline girlie fr fr 🫶

👑 DESCRIPTION 👑

so basically: bamconsensus reads a BAM, SAM or CRAM file and computes a rough consensus based on the alignments inside. that's the whole vibe. 💅

⚠️ your input file needs to be sorted in coordinate order. not optional, not negotiable, she will not be slaying otherwise.

the consensus gets written as an alignment file on the standard output channel. yes, stdout. redirect it, queen. 🎀

the sequence names in the output file are structured like this:

contig_A_B_C_D_E

where — and this is the important part, don't skip it —

  • A is the numeric reference id (0 based) 🔢
  • B is the name of the reference sequence as given in the BAM header 📛
  • C is a numerical contig id within the contigs for a given reference id 🧮
  • D is the start position on the reference sequence (inclusive) ⬅️
  • E is the end position on the reference sequence (exclusive) ➡️

the reference key specifying the name of a FastA reference sequence file is required. like, mandatory mandatory. 🙈

the consensus is constructed by computing heavy paths in local DeBruijn graphs. consequently it is usually a patchwork of the haplotypes present for diploid/polyploid genomes. so she's a collage, she's eclectic, she's doing her best, and honestly? iconic. 🌈

💜 the key=value pairs you can give 💜

the following key=value pairs can be given:

  • reference=<ref.fasta> — reference FastA file (required, bestie, do not forget her) 🌸
  • verbose=<1> — valid values are:
    1. 1: print progress report on standard error
    2. 0: do not print progress report
  • T=<filename> — set the prefix for temporary file names 🗂️
  • k=<32> — k-mer size used for consensus computation (maximum 32). that's the ceiling, don't push it 💀
  • minlen=<50> — minimum length of alignments used (default 50). short alignments, we don't know her 🙅‍♀️
  • inputformat=<bam> — input format 📥
  • range=<> — input range to be processed. this option is only valid if the input is a coordinate sorted and indexed BAM file 👑

🎀 AUTHOR 🎀

Written by German Tischler-Höhle. 💖

🐛 REPORTING BUGS 🐛

found a bug? don't be shy, report bugs to <germant@miltenyibiotec.de> 📧

Copyright © 2019 German Tischler. License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>

This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

not me reminding you that there is literally no warranty 😭 read it, internalize it, live it.

and that's the whole page, bestie! this one comes from BIOBAMBAM, dated August 2019, and it's BAMCONSENSUS(1) — go forth and compute that rough consensus, you absolute main character 👑✨💅

📦 where this page comes from