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 (2013-05-25 at
       17:45:01)

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

       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)