gmt music proximity

NAME

gmt music proximity - Perform a proximity analysis on a list of mutations.

VERSION

This document describes gmt music proximity version 0.04 (2018-07-05 at 09:17:13)

SYNOPSIS

gmt music proximity --maf-file=? --output-file=? --output-dir=? [--max-proximity=?] [--skip-non-coding] [--skip-silent]

 ... music proximity \
        --maf-file input_dir/myMAF.tsv \
        --output-dir output_dir/ \
        --max-proximity 15

REQUIRED ARGUMENTS

maf-file Text

List of mutations using TCGA MAF specifications v2.3

output-file Text

TODO

output-dir Text

Directory where output files will be written

OPTIONAL ARGUMENTS

max-proximity Text

Maximum allowed AA distance between 2 mutations

Default value '7' if not specified

skip-non-coding Boolean

Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

noskip-non-coding Boolean

Make skip-non-coding 'false'

skip-silent Boolean

Skip silent mutations from the provided MAF file

Default value 'true' if not specified

noskip-silent Boolean

Make skip-silent 'false'

DESCRIPTION

This module first calculates the amino acid position of each mutation in the MAF file within its respective transcript. Then, for each mutation, two values are calculated: 1) the number of other mutations on the same transcript within the proximity limit set by the max-proximity input parameter, and 2) the distance to the closest other mutation in this nearby set. Only mutations which have another mutation within close proximity are reported in the output-file.

In addition to the standard version 2.3 MAF headers, there needs to be 3 columns appended. These column headers in the MAF must have these names in the header in order for the tool to find them:
transcript_name - the transcript name, such as NM_000028
amino_acid_change - the amino acid change, such as p.R290H
c_position - the nucleotide position changed, such as c.869

The output is generated with the following column headers: Mutations_Within_Proximity, Nearest_Mutation, Gene, Transcript, Affected_Amino_Acid(s), Chr, Start, Stop, Ref_Allele, Var_Allele, Sample

AUTHORS

 Nathan D. Dees, Ph.D.
 Dan Koboldt, M.S.
 Cyriac Kandoth, Ph.D.