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GENOME-MUSIC-BMR-CALC-BMR(1p) User Contributed Perl Documentation GENOME-MUSIC-BMR-CALC-BMR(1p)

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

TODO
Tab delimited list of ROIs [chr start stop gene_name] (See DESCRIPTION)
TODO
Path to reference sequence in FASTA format
Tab delimited list of BAM files [sample_name normal_bam tumor_bam] (See DESCRIPTION)
Directory where output files will be written (Use the same one used with calc-covg)
List of mutations using TCGA MAF specification v2.3

OPTIONAL ARGUMENTS

Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

Make skip-non-coding 'false'
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

Make skip-silent 'false'
Number of clusters of samples with comparable BMRs (See DESCRIPTION)

Default value '1' if not specified

Report each skipped mutation, not just how many

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

Make show-skipped 'false'
Group truncational mutations as a separate category

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

Make separate-truncations 'false'
Multiple mutations of a gene in the same sample are treated as 1

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

Make merge-concurrent-muts 'false'
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

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)

2018-07-05 perl v5.26.2