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

       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)