OnWorks favicon

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

Run genome-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 genome-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



genome music bmr calc-covg-helper - Uses calcRoiCovg.c to count covered bases per-gene for
a tumor-normal pair of BAMs.


This document describes genome music bmr calc-covg-helper version 0.04 (2016-01-01 at


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


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

Free Servers & Workstations

Download Windows & Linux apps

Linux commands

  • 1
    abidiff - compare ABIs of ELF files
    abidiff compares the Application Binary
    Interfaces (ABI) of two shared libraries
    in ELF format. It emits a meaningful
    Run abidiff
  • 2
    abidw - serialize the ABI of an ELF
    file abidw reads a shared library in ELF
    format and emits an XML representation
    of its ABI to standard output. The
    emitted ...
    Run abidw
  • 3
    cppo - lightweight cpp-like
    preprocessor for OCaml ...
    Run cppo
  • 4
    cppunit-config - script to get
    information about the installed version
    of cppunit ...
    Run cppunit-config
  • 5
    fwb_ipt - Policy compiler for Cisco IOS
    ACL ...
    Run fwb_iosacl
  • 6
    fwb_ipf - Policy compiler for ipfilter ...
    Run fwb_ipf
  • More »