genome music bmr calc-wig-covg

NAME

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

VERSION

       This document describes genome music bmr calc-wig-covg version 0.04 (2013-05-25 at
       17:45:01)

SYNOPSIS

       genome 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.

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)