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PROGRAM:

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 (2016-01-01 at
23:10:19)

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


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

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