GMT-MUSIC-BMR-CALC-COVG-HELPER(1p) | User Contributed Perl Documentation | GMT-MUSIC-BMR-CALC-COVG-HELPER(1p) |
gmt music bmr calc-covg-helper¶
NAME¶
gmt music bmr calc-covg-helper - Uses calcRoiCovg.c to count covered bases per-gene for a tumor-normal pair of BAMs.
VERSION¶
This document describes gmt music bmr calc-covg-helper version 0.04 (2018-07-05 at 09:17:13)
SYNOPSIS¶
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
REQUIRED ARGUMENTS¶
- 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)
OPTIONAL ARGUMENTS¶
- 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
DESCRIPTION¶
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.
ARGUMENTS¶
- "sample-name path/to/normal_bam path/to/tumor_bam"
LICENSE¶
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.
AUTHORS¶
Cyriac Kandoth, Ph.D.
SEE ALSO¶
genome-music-bmr(1), genome-music(1), genome(1)
2018-07-05 | perl v5.26.2 |