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PROGRAM:

NAME


genome music bmr calc-bmr - Calculates mutation rates given per-gene coverage (from "music
bmr calc-covg"), and a mutation list

VERSION


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

SYNOPSIS


genome music bmr calc-bmr --bmr-output=? --roi-file=? --gene-mr-file=?
--reference-sequence=? --bam-list=? --output-dir=? --maf-file=? [--skip-non-coding]
[--skip-silent] [--bmr-groups=?] [--show-skipped] [--separate-truncations]
[--merge-concurrent-muts] [--genes-to-ignore=?]

... music bmr calc-bmr \
--bam-list input_dir/bam_list \
--maf-file input_dir/myMAF.tsv \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
--roi-file input_dir/all_coding_exons.tsv

... music bmr calc-bmr \
--bam-list input_dir/bam_list \
--maf-file input_dir/myMAF.tsv \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
--roi-file input_dir/all_coding_exons.tsv \
--genes-to-ignore GENE1,GENE2

REQUIRED ARGUMENTS


bmr-output Number
TODO

roi-file Text
Tab delimited list of ROIs [chr start stop gene_name] (See DESCRIPTION)

gene-mr-file Text
TODO

reference-sequence Text
Path to reference sequence in FASTA format

bam-list Text
Tab delimited list of BAM files [sample_name normal_bam tumor_bam] (See DESCRIPTION)

output-dir Text
Directory where output files will be written (Use the same one used with calc-covg)

maf-file Text
List of mutations using TCGA MAF specification v2.3

OPTIONAL ARGUMENTS


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'

bmr-groups Integer
Number of clusters of samples with comparable BMRs (See DESCRIPTION)

Default value '1' if not specified

show-skipped Boolean
Report each skipped mutation, not just how many

Default value 'false' (--noshow-skipped) if not specified

noshow-skipped Boolean
Make show-skipped 'false'

separate-truncations Boolean
Group truncational mutations as a separate category

Default value 'false' (--noseparate-truncations) if not specified

noseparate-truncations Boolean
Make separate-truncations 'false'

merge-concurrent-muts Boolean
Multiple mutations of a gene in the same sample are treated as 1

Default value 'false' (--nomerge-concurrent-muts) if not specified

nomerge-concurrent-muts Boolean
Make merge-concurrent-muts 'false'

genes-to-ignore Text
Comma-delimited list of genes to ignore for background mutation rates

DESCRIPTION


Given a mutation list (MAF), and per-gene coverage data calculated using "music bmr calc-
covg"), this script calculates overall Background Mutation Rate (BMR) and BMRs in the
categories of AT/CG/CpG Transitions, AT/CG/CpG Transversions, and Indels. An optional
category for truncational mutations can also be specified. The script generates a file
with per-gene mutation rates that can be used with the tool that tests for significantly
mutated genes (music smg).

ARGUMENTS


--roi-file
The regions of interest (ROIs) of each gene are typically regions targeted for
sequencing or are merged exon loci (from multiple transcripts) of genes with 2-bp
flanks (splice junctions). ROIs from the same chromosome must be listed adjacent to
each other in this file. This allows the underlying C-based code to run much more
efficiently and avoid re-counting bases seen in overlapping ROIs (for overall covered
base counts). For per-gene base counts, an overlapping base will be counted each time
it appears in an ROI of the same gene. To avoid this, be sure to merge together
overlapping ROIs of the same gene. BEDtools' mergeBed can help if used per gene.
--reference-sequence
The reference sequence in FASTA format. If a reference sequence index is not found
next to this file (a .fai file), it will be created.
--bam-list
Provide a file containing sample names and normal/tumor BAM locations for each. Use
the tab- delimited format [sample_name normal_bam tumor_bam] per line. Additional
columns like clinical data are allowed, but ignored. The sample_name must be the same
as the tumor sample names used in the MAF file (16th column, with the header
Tumor_Sample_Barcode).
--bmr-groups
Ideally, we want to test the mutation rate (MR) of a gene in a sample against the
background mutation rate (BMR) across that sample. But if the BMRs of some samples are
comparable, we can instead test the MR of a gene across a group of samples with
comparable BMR, against the overall BMR of that group. This argument specifies how
many such groups you want to cluster samples into. By default, it is assumed that all
samples have comparable BMRs (bmr-groups = 1).
--output-dir
This should be the same output directory used when running "music bmr calc-covg". The
following outputs of this script will also be created/written: overall_bmrs: File
containing categorized overall background mutation rates. gene_mrs: File containing
categorized per-gene mutation rates.
--genes-to-ignore
A comma-delimited list of genes to ignore for overall BMR calculations. List genes
that are known factors in this disease and whose mutations should not be classified as
background.

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