gmt music bmr calc-covg-helper - Uses calcRoiCovg.c to count covered bases
per-gene for a tumor-normal pair of BAMs.
This document describes gmt music bmr calc-covg-helper version 0.04 (2016-01-01
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=?]
... 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 Text
- Tab delimited list of ROIs [chr start stop gene_name] (See
- 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)
- output-file Text
- Output file path. Specify either output-file or
- output-dir Text
- Output directory path. Specify either output-file or
- normal-min-depth Integer
- The minimum read depth to consider a Normal BAM base as
Default value '6' if not specified
- tumor-min-depth Integer
- The minimum read depth to consider a Tumor BAM base as
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 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.
- 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.
- The reference sequence in FASTA format. If a reference
sequence index is not found next to this file (a .fai file), it will be
- "sample-name path/to/normal_bam
- 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 GNU Public License (LGPL) version 3. See the
associated LICENSE file in this distribution.
Cyriac Kandoth, Ph.D.