genome-music-bmr-calc-bmr (1p)

This document describes genome music bmr calc-bmr version 0.04 (2013-05-14 at 16:03:04)

genome music bmr calc-bmr --roi-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

roi-file Text

Tab delimited list of ROIs [chr start stop gene_name] (See \s-1DESCRIPTION\s0)

reference-sequence Text

Path to reference sequence in \s-1FASTA\s0 format

bam-list Text

Tab delimited list of \s-1BAM\s0 files [sample_name normal_bam tumor_bam] (See \s-1DESCRIPTION\s0)

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 \s-1TCGA\s0 \s-1MAF\s0 specification v2.3

skip-non-coding Boolean

Skip non-coding mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified

skip-silent Boolean

Skip silent mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified

bmr-groups Integer

Number of clusters of samples with comparable BMRs (See \s-1DESCRIPTION\s0) 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

separate-truncations Boolean

Group truncational mutations as a separate category Default value 'false' (--noseparate-truncations) if not specified

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

genes-to-ignore Text

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

Given a mutation list (\s-1MAF\s0), and per-gene coverage data calculated using \*(L"music bmr calc-covg\*(R"), this script calculates overall Background Mutation Rate (\s-1BMR\s0) 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).

--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 \s-1ROI\s0 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 \s-1FASTA\s0 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 \s-1BAM\s0 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 \s-1MAF\s0 file (16th column, with the header Tumor_Sample_Barcode).

--bmr-groups

Ideally, we want to test the mutation rate (\s-1MR\s0) of a gene in a sample against the background mutation rate (\s-1BMR\s0) across that sample. But if the BMRs of some samples are comparable, we can instead test the \s-1MR\s0 of a gene across a group of samples with comparable \s-1BMR\s0, against the overall \s-1BMR\s0 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

--genes-to-ignore

A comma-delimited list of genes to ignore for overall \s-1BMR\s0 calculations. List genes that are known factors in this disease and whose mutations should not be classified as background.

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

It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3. See the associated \s-1LICENSE\s0 file in this distribution.

Cyriac Kandoth, Ph.D.

genome-music-bmr(1), genome-music(1), genome(1)