GENOME-MUSIC(1p)

📦 version 0.04, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

👑 genome music 👑

okay bestie, welcome to the genome music manual page, aka the GENOME-MUSIC(1p) glow-up. she's a Perl situation, she's from User Contributed Perl Documentation, and she's about to tell you everything about finding mutational significance in cancer. let's go 💅

✨ NAME ✨

genome music — Mutational Significance in Cancer (Cancer Mutation Analysis). that's the whole vibe. 🎀

🌸 VERSION 🌸

this doc describes genome music version 0.04 (dated 2020-11-06 at 21:54:23). yes she's a little vintage, she's still iconic. ✨

🦋 SYNOPSIS 🦋

genome music ...

that's it. that's the synopsis. the ... is doing a lot of heavy lifting and honestly? respect. 💜

💖 DESCRIPTION 💖

so the MuSiC suite is a set of tools whose whole main character moment is discovering the significance of somatic mutations found within a given cohort of cancer samples — and doing it with respect to a variety of external data sources. no cap. 🔥

the standard inputs she needs from you are:

  1. mapped reads in BAM format
  2. predicted or validated SNVs or indels in mutation annotation format (MAF)
  3. a list of regions of interest (typically the boundaries of coding exons)
  4. any relevant numeric or categorical clinical data.

now, the formats for inputs 3. and 4. — because bestie, these two have ✨rules✨:

3. Regions of Interest File:

  • Do not use headers
  • 4 columns, which are [chromosome start-position(1-based) stop-position(1-based) gene_name]

4. Clinical Data Files:

  • Headers are required
  • At least 1 sample_id column and 1 attribute column, with the format being [sample_id clinical_data_attribute clinical_data_attribute ...]
  • The sample_id must match the sample_id listed in the MAF under "Tumor_Sample_Barcode" for relating the mutations of this sample.
  • The header for each clinical_data_attribute will appear in the output file to denote relationships with the mutation data from the MAF.
🫶 okay so, lowkey important: that sample_id matching thing is not optional, it's how the clinical data and the mutation data find each other. it's giving soulmates, but make it data integrity.

descriptions for the usage of each tool (each sub-command) can be found separately. go look them up individually, they each get their own page. 💅

and the play command? she runs all of the sub-commands serially on a selected input set. one command, full ensemble cast, main character energy for days. 👑

🌈 LICENSE 🌈

Copyright (C) 2007-2011 Washington University in St. Louis.

It is released under the Lesser GNU Public License (LGPL) version 3. See the associated LICENSE file in this distribution.

🧚 AUTHORS 🧚

This software is developed by the analysis and engineering teams at The Genome Institute at Washington University School of Medicine in St. Louis, with funding from the National Human Genome Research Institute. Richard K. Wilson, P.I.

The primary authors of the MuSiC suite are:

 Nathan D. Dees, Ph.D.
 Cyriac Kandoth, Ph.D.
 Dan Koboldt, M.S.
 William Schierding, M.S.
 Michael Wendl, Ph.D.
 Qunyuan Zhang, Ph.D.
 Thomas B. Mooney, M.S.

genuinely obsessed with all of them, they built this whole thing. 🙈💖

⭐ CREDITS ⭐

The MuSiC suite uses tabix, by Heng Li. See http://samtools.sourceforge.net/tabix.shtml.

MuSiC depends on copies of data from the following databases, packaged in a form useable for quick analysis:

seven databases, all packaged up and ready to go. she's prepared. 🌸

💀 BUGS 💀

For defects with any software in the genome namespace, contact genome-dev ~at~ genome.wustl.edu.

😭 not me telling you to actually email them if something's broken — but fr fr, do it. and remember, ~at~ means @. don't send it to the literal tilde-at-tilde, bestie.

🎀 SEE ALSO 🎀

genome(1)

and that's the whole page, you made it to the end, so proud of you 🫶 the footer says perl v5.30.3, dated 2020-11-06, and this is page GENOME-MUSIC(1p) — so basically, yeah, perl did that, and she ate. periodt. 💅✨

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