genome music bmr calc-covg-helper

NAME

genome 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 genome music bmr calc-covg-helper version 0.04 (2018-07-05 at 09:17:13)

SYNOPSIS

genome 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

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
normal-tumor-bam-pair Text: Tab delimited line with sample name, path to normal bam file, and path to tumor bam file (See Description)

OPTIONAL ARGUMENTS

output-file Text: Output file path. Specify either output-file or output-directory.
output-dir Text: Output directory path. Specify either output-file or output-directory
normal-min-depth Integer: The minimum read depth to consider a Normal BAM base as covered
Default value '6' if not specified
tumor-min-depth Integer: The minimum read depth to consider a Tumor BAM base as covered
Default value '8' if not specified
min-mapq Integer: 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

--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.

--normal-tumor-bam-pair

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

--output-file

Specify an output file where the per-ROI covered base counts will be written

LICENSE

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.