nilesh-iiita/calc-roi-covg

Given two BAM files, a reference sequence, and regions of interest, count the AT, CG, or CpG sites with sufficient read-depth in both BAMs.

calcRoiCovg

Given two BAM files, a reference sequence, and regions of interest, count the AT/CG/CpG sites with sufficient read-depth in both BAMs.

Usage

calcRoiCovg <bam1> <bam2> <roi_file> <ref_seq_fasta> <output_file> [min_depth_bam1 min_depth_bam2 min_mapq]

Defaults: min_depth_bam1 = 6, min_depth_bam2 = 8, min_mapq = 20
NOTE: ROI file *must* be sorted by chromosome/contig names

This tool was originally designed to count base-pairs that have sufficient read-depth for variant calling across two BAM files (case vs control). The base-pairs are further classified into AT, CG (non-CpG), and CpG sites, with respect to the provided reference sequence. The resulting coverage stats are reported for each region of interest (ROI).

Sample ROI files can be found under the 'data' subdirectory. Note that they use 1-based loci, and must be sorted by chromosome or contig names.

Install

The Makefile assumes that you have the samtools source code in an environment variable $SAMDIR. If you don't know what that means, then simply follow these steps from any directory that you have permissions to write into:

Install some prerequisite packages if you are using Debian or Ubuntu:

sudo apt-get install git libbam-dev zlib1g-dev

If you are using Fedora, CentOS or RHEL, you'll need these packages instead:

sudo yum install git samtools-devel zlib-devel

Clone the samtools and calc-roi-covg repos, and build the calcRoiCovg binary:

git clone https://github.com/samtools/samtools.git
export SAMDIR=$PWD/samtools
git clone https://github.com/ding-lab/calc-roi-covg.git
cd calc-roi-covg
make

Now you can put the resulting binary where your $PATH can find it. If you have su permissions, then I recommend dumping it in the system directory for locally compiled packages:

sudo mv calcRoiCovg /usr/local/bin/