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PROGRAM:

NAME


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

VERSION


This document describes genome music bmr calc-covg version 0.04 (2016-01-01 at 23:10:18)

SYNOPSIS


genome music bmr calc-covg --gene-covg-dir=? --roi-file=? --reference-sequence=?
--bam-list=? --output-dir=? [--cmd-list-file=?] [--cmd-prefix=?] [--normal-min-depth=?]
[--tumor-min-depth=?] [--min-mapq=?]

General usage:

... music bmr calc-covg \
--bam-list input_dir/bam_list \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
--roi-file input_dir/all_coding_exons.tsv

To create a list of commands that will allow the processing of each tumor-normal pair in
parallel with an LSF job scheduler:

... music bmr calc-covg \
--bam-list input_dir/bam_list \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
--roi-file input_dir/all_coding_exons.tsv \
--cmd_list_file parallelizable_commands \
--cmd_prefix bsub

In the above case, the commands printed into the output file "parallelizable_commands" can
be run in parallel. After they complete, rerun this script as printed directly below
(--cmd_list_file and --cmd_prefix have been removed) to merge the parallelized
calculations:

... music bmr calc-covg \
--bam-list input_dir/bam_list \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
--roi-file input_dir/all_coding_exons.tsv

REQUIRED ARGUMENTS


gene-covg-dir Text
Directory where per-sample gene coverage files are located

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

bam-list Text
Tab delimited list of BAM files [sample_name normal_bam tumor_bam] (See Description)

output-dir Text
Directory where output files and subdirectories will be written

OPTIONAL ARGUMENTS


cmd-list-file Text
A file to write calcRoiCovg commands to (See Description)

cmd-prefix Text
A command that submits a job to your cluster (See Description)

normal-min-depth Integer
The minimum read depth to consider a Normal BAM base as covered

tumor-min-depth Integer
The minimum read depth to consider a Tumor BAM base as covered

min-mapq Integer
The minimum mapping quality of reads to consider towards read depth counts

DESCRIPTION


This script counts bases with sufficient coverage in the ROIs of each gene in the given
pairs 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 for each sample,
but covered bases that lie within overlapping ROIs are not counted more than once towards
these total counts.

By default, this script runs a C-based tool named calcRoiCovg for each sample one after
another, taking ~30 mins per sample to generate per-ROI covered base counts. If the
results of calcRoiCovg for a sample already exists in the output subdirectory roi_covgs,
re-calculation is skipped. This allows you to run your own calcRoiCovg jobs in parallel or
on multiple machines (Keep reading).

Speed things up by running calcRoiCovg jobs in parallel: If a compute cluster or multiple
machines are available, run this script twice as follows:

· Define cmd-list-file and cmd-prefix to generate a file with commands that can be
submitted to a cluster or run manually. These jobs will write per-ROI base counts in a
subdirectory roi_covgs.

· After all the parallelized calcRoiCovg jobs are completed, run this script again to
add them up and generate the final per-gene base counts in a subdirectory gene_covgs.
Remember to remove the cmd-list-file and cmd-prefix arguments or you will just be re-
creating a list of commands.

ARGUMENTS


--roi-file
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.
--reference-sequence
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.
--bam-list
Provide a file containing sample names and normal/tumor BAM locations for each. Use
the tab- delimited format [sample_name normal_bam tumor_bam] per line. Additional
columns like clinical data are allowed, but ignored. The sample_name must be the same
as the tumor sample names used in the MAF file (16th column, with the header
Tumor_Sample_Barcode).
--output-dir
Specify an output directory where the following will be created/written: roi_covgs:
Subdirectory containing per-ROI covered base counts for each sample. gene_covgs:
Subdirectory containing per-gene covered base counts for each sample. total_covgs:
File containing the overall non-overlapping coverages per sample.
--cmd-list-file
Specify a file into which a list of calcRoiCovg jobs will be written to. These can be
scheduled in parallel, and will write per-ROI covered base-counts into the output
subdirectory roi_covgs. If cmd-list-file is left unspecified, this script runs
calcRoiCovg per sample one after another, taking ~30 mins per sample, but it skips
samples whose output is already in roi_covgs.
--cmd-prefix
Specify a job submission command that will be prefixed to each command in cmd-list-
file. This makes batch submission easier. Just run the cmd-list-file file as a shell
script to submit jobs. cmd-prefix is "bsub" if your cluster uses the LSF job
scheduler, or "qsub" in Torque. Add arguments as necessary. For example, "bsub -M 4GB"
sets a soft memory limit of 4GB.

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