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).