OnWorks favicon

gmt-music-bmr-calc-covg-helperp - Online in the Cloud

Run gmt-music-bmr-calc-covg-helperp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmt-music-bmr-calc-covg-helperp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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 at


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


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)


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


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 created.
"sample-name path/to/normal_bam path/to/tumor_bam"
Specify an output file where the per-ROI covered base counts will be written

Use gmt-music-bmr-calc-covg-helperp online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    Download Eclipse Tomcat Plugin
  • 2
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 3
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 4
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 5
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • 6
    eSpeak: speech synthesis
    eSpeak: speech synthesis
    Text to Speech engine for English and
    many other languages. Compact size with
    clear but artificial pronunciation.
    Available as a command-line program with
    many ...
    Download eSpeak: speech synthesis
  • More »

Linux commands