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PROGRAM:

NAME


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

VERSION


This document describes genome music proximity version 0.04 (2016-01-01 at 23:10:18)

SYNOPSIS


genome 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 folowing 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.

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