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=?]
... 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 \
Tab delimited list of ROIs [chr start stop gene_name] (See Description)
Path to reference sequence in FASTA format
Tab delimited line with sample name, path to normal bam file, and path to tumor bam
file (See Description)
Output file path. Specify either output-file or output-directory.
Output directory path. Specify either output-file or output-directory
The minimum read depth to consider a Normal BAM base as covered
Default value '6' if not specified
The minimum read depth to consider a Tumor BAM base as covered
Default value '8' if not specified
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
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