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HMM Copy Utils

Author: Daniel Lai dalai@bccrc.ca Department of Molecular Oncology, BC Cancer Research Agency Date: August 02, 2011

Overview

This repo provides tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.

Installation

Using CMake

Requires cmake installed and on PATH (http://www.cmake.org/). In the source directory, install as follows:

cmake .
make

Should result in main binaries in /bin and useful binaries in /util

Usage

mapCounter

fast average mappability counter using BigWig files

Overview:

mapCounter is a small program for calculating average mappability for non-overlapping windows of fixed width across all sequences (i.e. chromosomes) present in a BigWig file. It is built mainly on top of an independent subset of files obtained from the UCSC Genome Browser source code (i.e. kent library) made available by Jim Kent. Generating average mappability files in 1000 base windows (default) on hg18 took 160 seconds on a 3.06 GHz Intel Core 2 Duo with 8GB RAM.

Features:

  • Average mappability calculation for fixed non-overlapping windows

CLI:

Usage: ./mapCounter [options] <BigWig file>

Options:
	-w, --window <int>       Specify the size of non-overlapping windows [1000]
	-l, --list               List all chromosomes in BigWig file
	-s, --sequence <string>  Specify the entries and order of sequences to analyze [ALL],
							 the <string> should be a comma-delimited list (NO spaces)
Example:
	./mapCounter -w 100000 -s 1,3,5,X hg18.bw > hg18.map.seg

gcCounter

Overview:

gcCounter is a small program for calculating GC content for non-overlapping windows of fixed width across all sequences (i.e. chromosomes) present in a FASTA reference file. It is built mainly on top of the fastahack source code made available by Erik Garrison erik.garrison@bc.edu of the Marth Lab at Boson College at GitHub (https://github.com/ekg/fastahack). Calculating the GC content in windows of 1000 on hg18 took 54 seconds on a 3.06 GHz Intel Core 2 Duo with 8GB RAM.

Features:

  • FASTA index (.fai) generation for FASTA files (~30 seconds for hg18 on 3GHz Core 2 Duo)
  • GC content calculation for fixed non-overlapping windows
  • N content calculation (anything not ACGT) for fixed non-overlapping windows

CLI:

Usage: ./gcCounter [options] <FASTA reference>

Options:
	-w, --window <int>       Specify the size of non-overlapping windows [1000]
	-l, --list               List all chromosomes in FASTA reference file
	-s, --sequence <string>  Specify the entries and order of sequences to analyze [ALL],
							 the <string> should be a comma-delimited list (NO spaces)
Example:
	./gcCounter -w 100000 -s 1,3,5,X hg18.fasta > hg18.gc.seg

readCounter

Fast and memory efficient counting of reads in BAM files

Overview:

mapCounter is a small program for counting the number of reads in non-overlapping windows of fixed width directly from BAM files. It is build on top of the BamTools API made available by Derek Barnett on GitHub (https://github.com/pezmaster31/bamtools).

Features:

  • Average mappability calculation for fixed non-overlapping windows

CLI:

Usage: ./readCounter [options] <BAM file>

Options:
    -w, --window <int>       Specify the size of non-overlapping windows [1000]
    -q, --quality <int>      Specify the mapping quality value below which reads are ignored

    -l, --list               List all chromosomes in BAM reference file
    -s, --sequence <string>  Specify the entries and order of sequences to analyze [ALL],
                             the <string> should be a comma-delimited list (NO spaces)

    -b, --build              Build BAM index for file (same index format as SAMtools)
Example:
    ./readCounter -w 100 -s 1,3,5,X aligned_reads.bam > readcounts.seg