genome-music-bmr-calc-covg-helper (1p)

This document describes genome music bmr calc-covg-helper version 0.04 (2013-05-14 at 16:03:04)

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

roi-file Text

Tab delimited list of ROIs [chr start stop gene_name] (See Description)

reference-sequence Text

Path to reference sequence in \s-1FASTA\s0 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)

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 \s-1BAM\s0 base as covered Default value '6' if not specified

tumor-min-depth Integer

The minimum read depth to consider a Tumor \s-1BAM\s0 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

This script counts bases with sufficient coverage in the ROIs of each gene in the given pair of tumor-normal \s-1BAM\s0 files and categorizes them into - \s-1AT\s0, \s-1CG\s0 (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.

--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 \s-1ROI\s0 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 \s-1FASTA\s0 format. If a reference sequence index is not found next to this file (a .fai file), it will be created.

--normal-tumor-bam-pair

--output-file

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

Copyright (C) 2010-2011 Washington University in St. Louis.

It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3. See the associated \s-1LICENSE\s0 file in this distribution.

Cyriac Kandoth, Ph.D.

genome-music-bmr(1), genome-music(1), genome(1)