A copy number variant caller based on this paper and implemented on top of ADAM.
References
Nord, Alex S., et al. "Accurate and exact CNV identification from targeted high-throughput sequence data." BMC genomics 12.1 (2011): 184.
Massie, Matt, et al. ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing. Technical Report UCB/EECS-2013-207, EECS Department, University of California, Berkeley, 2013.
To build
This project uses Maven and produces a shaded uber-jar. To build, run:
mvn package
From the repository root.
To run
The minimum arguments required to run are:
$ java -Xmx2g -jar target/cnv-0.0.1.jar
Argument "READS" is required
READS : ADAM read-oriented data
TARGETS : Target probe input
VARIANTS : BED output
E.g.,
java -Xmx2g -jar target/cnv-0.0.1.jar reads.bam probes.txt cnvs.bed
Running the command without any arguments produces full debug output.