gmt music bmr calc-covg-helper¶
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 (2013-05-14
at 16:03:05)
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
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)