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PROGRAM:

NAME


gmt music bmr calc-wig-covg - Count covered bases per-gene for each given wiggle track
format file.

VERSION


This document describes gmt music bmr calc-wig-covg version 0.04 (2016-01-01 at 23:10:19)

SYNOPSIS


gmt music bmr calc-wig-covg --roi-file=? --reference-sequence=? --wig-list=?
--output-dir=?

General usage:

... music bmr calc-wig-covg \
--wig-list input_dir/wig_list \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
--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

wig-list Text
Tab-delimited list of WIG files [sample_name wig_file] (See Description)

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

DESCRIPTION


This script counts bases with sufficient coverage in the ROIs of each gene from given
wiggle track format 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.

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). 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.
--wig-list
Provide a file containing sample names and the wiggle track format file locations for
each. Use the tab-delimited format [sample_name wig_file] 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.

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