Perform a proximity analysis on a list of mutations.
This document describes gmt music proximity version 0.04 (2013-05-14 at 16:03:04)
gmt music proximity --maf-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
List of mutations using \s-1TCGA\s0 \s-1MAF\s0 specifications v2.3
Directory where output files will be written
Maximum allowed \s-1AA\s0 distance between 2 mutations Default value '7' if not specified
Skip non-coding mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified
Skip silent mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified
This module first calculates the amino acid position of each mutation in the \s-1MAF\s0 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 \s-1MAF\s0 headers, there needs to be 3 columns appended. These column headers in the \s-1MAF\s0 must have these names in the header in order for the tool to find them:
transcript_name - the transcript name, such as \s-1NM_000028\s0
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 folowing column headers: Mutations_Within_Proximity, Nearest_Mutation, Gene, Transcript, Affected_Amino_Acid(s), Chr, Start, Stop, Ref_Allele, Var_Allele, Sample
Nathan D. Dees, Ph.D. Dan Koboldt, M.S. Cyriac Kandoth, Ph.D.