GMT-MUSIC(1p)

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

🎀 gmt music — bestie edition 🎀

okay so you're looking at the gmt music page, which lives in the User Contributed Perl Documentation corner of the manual universe (it's GMT-MUSIC(1p), iykyk). it's the Mutational Significance in Cancer situation — aka Cancer Mutation Analysis — and it's about to eat, no cap. 💅

✨ NAME ✨

gmt music — Mutational Significance in Cancer (Cancer Mutation Analysis)

🌸 VERSION 🌸

this doc is describing gmt music version 0.04, and it's dated 2020-11-06 at 21:54:23. vintage but still iconic fr.

🦋 SYNOPSIS 🦋

gmt music ...

yeah that's the whole thing. three dots of pure potential. the ... is doing main character work here. 👑

💖 DESCRIPTION 💖

so the MuSiC suite is a whole set of tools, and their collective dream is discovering the significance of somatic mutations found inside a given cohort of cancer samples, and doing it relative to a whole buffet of external data sources. very "we're analyzing everything, bestie" energy.

here's the standard input lineup you need to bring to the party:

  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.

🧚 the formats for inputs 3. and 4. (yes, they have rules) 🧚

3. Regions of Interest File:

  • Do not use headers. like, none. zero. don't even think about it. 🙈
  • 4 columns, and they go exactly like this: [chromosome start-position(1-based) stop-position(1-based) gene_name]

4. Clinical Data Files:

  • Headers are required (opposite vibe from #3, keep up 💀)
  • at least 1 sample_id column and 1 attribute column, formatted like: [sample_id clinical_data_attribute clinical_data_attribute ...]
  • the sample_id must match the sample_id listed in the MAF under "Tumor_Sample_Barcode" — that's how we relate the mutations of this sample, okay? it's giving matching bracelets. 🫶
  • the header for each clinical_data_attribute will appear in the output file to denote relationships with the mutation data from the MAF.

descriptions for the usage of each tool (each sub-command) can be found separately. go hunt those down, they each have their own lore. 🔍

and the play command? it runs all of the sub-commands serially on a selected input set. one after another after another. a whole marathon, no intermission. 🔥

👑 LICENSE 👑

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

it's released under the Lesser GNU Public License (LGPL) version 3. see the associated LICENSE file in this distribution for the full legal tea. ☕

🌈 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. — we stan a principal investigator. 💜

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.

absolute legends, every single one. 🏆

⭐ CREDITS ⭐

the MuSiC suite uses tabix, by Heng Li. see http://samtools.sourceforge.net/tabix.shtml. shoutout, king. 🫡

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

the database crossover event of the century, honestly. 💫

💀 BUGS 💀

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

(not me telling you to report bugs — please do, they want to know 😭)

🔥 SEE ALSO 🔥

okay bestie, that's the whole page. go be significant. 💅✨

sign-off time: this lil doc came to you courtesy of perl v5.30.3, dated 2020-11-06, and it's the GMT-MUSIC(1p) page — so now you know the whole vibe. slay, stay mutated (respectfully), and go run some gmt music. 🎀🦋💖

📦 where this page comes from