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GMT-MUSIC-BMR-CALC-COVG-HELPER(1p) User Contributed Perl Documentation GMT-MUSIC-BMR-CALC-COVG-HELPER(1p)

gmt music bmr calc-covg-helper

NAME

gmt music bmr calc-covg-helper - Uses calcRoiCovg.c to count covered bases per-gene for a tumor-normal pair of BAMs.

VERSION

This document describes gmt music bmr calc-covg-helper version 0.04 (2018-07-05 at 09:17:13)

SYNOPSIS

gmt music bmr calc-covg-helper --roi-file=? --reference-sequence=? --normal-tumor-bam-pair=? [--output-file=?] [--output-dir=?] [--normal-min-depth=?] [--tumor-min-depth=?] [--min-mapq=?]

General usage:

 ... music bmr calc-covg-helper \
    --normal-tumor-bam-pair "sample-name path/to/normal_bam path/to/tumor_bam" \
    --reference-sequence input_dir/all_sequences.fa \
    --output-file output_file \
    --roi-file input_dir/all_coding_exons.tsv

REQUIRED ARGUMENTS

Tab delimited list of ROIs [chr start stop gene_name] (See Description)
Path to reference sequence in FASTA format
Tab delimited line with sample name, path to normal bam file, and path to tumor bam file (See Description)

OPTIONAL ARGUMENTS

Output file path. Specify either output-file or output-directory.
Output directory path. Specify either output-file or output-directory
The minimum read depth to consider a Normal BAM base as covered

Default value '6' if not specified

The minimum read depth to consider a Tumor BAM base as covered

Default value '8' if not specified

The minimum mapping quality of reads to consider towards read depth counts

Default value '20' if not specified

DESCRIPTION

This script counts bases with sufficient coverage in the ROIs of each gene in the given pair of tumor-normal BAM files and categorizes them into - AT, CG (non-CpG), and CpG counts. It also adds up these base-counts across all ROIs of each gene in the sample, but covered bases that lie within overlapping ROIs are not counted more than once towards these total counts.

ARGUMENTS

"sample-name path/to/normal_bam path/to/tumor_bam"

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