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genome music bmr calc-bmr

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 (2018-07-05 at 09:17:13)

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.

LICENSE

       Copyright (C) 2010-2011 Washington University in St. Louis.

       It is released under the Lesser GNU Public License (LGPL) version 3.  See the associated LICENSE file in
       this distribution.

AUTHORS

        Cyriac Kandoth, Ph.D.