|GMT-MUSIC-BMR-CALC-COVG-HELPER(1p)||User Contributed Perl Documentation||GMT-MUSIC-BMR-CALC-COVG-HELPER(1p)|
gmt music bmr calc-covg-helper¶
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 (2018-07-05 at 09:17:13)
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 input_dir/all_coding_exons.tsv
- 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.
- "sample-name path/to/normal_bam path/to/tumor_bam"
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.