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 (2013-05-14 at
16:03:04)
SYNOPSIS¶
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
REQUIRED ARGUMENTS¶
- roi-file Text
- Tab delimited list of ROIs [chr start stop gene_name] (See
DESCRIPTION)
- 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
- skip-silent Boolean
- Skip silent mutations from the provided MAF file
Default value 'true' if not specified
- 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
- 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
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.
SEE ALSO¶
genome-music-bmr(1),
genome-music(1),
genome(1)