gmt music bmr calc-wig-covg - Count covered bases per-gene for each given wiggle
track format file.
This document describes gmt music bmr calc-wig-covg version 0.04 (2016-01-01 at
gmt music bmr calc-wig-covg --roi-file=? --reference-sequence=? --wig-list=?
... music bmr calc-wig-covg \
--wig-list input_dir/wig_list \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
- roi-file Text
- Tab-delimited list of ROIs [chr start stop gene_name] (See
- reference-sequence Text
- Path to reference sequence in FASTA format
- wig-list Text
- Tab-delimited list of WIG files [sample_name wig_file] (See
- output-dir Text
- Directory where output files and subdirectories will be
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.
- 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.
- The reference sequence in FASTA format. If a reference
sequence index is not found next to this file (a .fai file), it will be
- 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).
- 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.
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.