Provided by: libgenome-model-tools-music-perl_0.04-4_all
gmt music proximity
gmt music proximity - Perform a proximity analysis on a list of mutations.
This document describes gmt music proximity version 0.04 (2018-07-05 at 09:17:13)
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
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
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'
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
Nathan D. Dees, Ph.D. Dan Koboldt, M.S. Cyriac Kandoth, Ph.D.