noam-hadar / bamdelbee

BAMdelbee is a novel tool for discovering homozygous deletions in Whole-exome-sequencing (WES) and whole-genome-sequencing (WGS) data. WES or WGS samples generated by the same method produce BAM files with similar alignment coverage across the genome. BAMdelbee locates homozygous deletions by pinpointing regions covered in all samples but the ones in question. We hereby demonstrate how our application can spot homozygous deletions absent from VCF files for being too vast, yet undetectable by chromosomal microarrays (CMA) for being too small. The application is freely available on our website and can run on a common laptop. Therefore, we recommend integrating it into WES and WGS interpretation pipelines for recessive diseases.

#Introduction
BAMdelbee is a novel tool for discovering homozygous deletions in Whole-exome-sequencing (WES) and whole-genome-sequencing (WGS) data. The application is based on the idea that WES or WGS samples generated by the same method produce BAM files with similar alignment coverage across the genome. BAMdelbee locates homozygous deletions by pinpointing regions covered in all samples but the ones in question. Our application can spot homozygous deletions absent from VCF files for being too vast, yet undetectable by chromosomal microarrays (CMA) for being too small. The application is freely available for research purposes and can run on a common laptop. The application is developed by Noam Hadar, a MD PhD student under the guidance of Prof. Ohad Birk, at the The Morris Kahn Laboratory of Human Genetics. We use BAMdelbee in every recessive disease study including WES and WGS and recommend doing so to address the blind spot that is not investigated using CMA and VCF files.

#Installation and user guide are available in the file "BAMdelbee-Instructions" and at:
birklab.bgu.ac.il/BAMdelbee