Zinfandel

detecting CNVs from low-pass whole genome shotgun data

Download: Zinfandel v0.9

Notes

The program requires 3 input files:

  1. Reference fasta file
  2. Mapview file - alignment from MAQ by Heng Li.
  3. Parameter file with genome type, prior estimated number of CNVs, average CNV size, depth coverage, and read size

Running the program

After compiling all the .java files, use command in the following format:
java Main -r reference.fasta -m mapview -p parameters

Contact

Yufeng Shen yshen@c2b2.columbia.edu