Large deletions in exome sequencing data

Question

[Ankit]

Hi everyone, Is there a method/pipeline or tools to get a hint about heterozygous large deletions (> 1kb) in exome sequencing and targeted panel seq data ? Is there a way apart from manual checking in IGV ?

[WouterDeCoster]

Googling exome sequencing structural variation will give you plenty of hits.

Answer 1

[Benn]

There are more tools available, I tried a few and had a good experience with R (CRAN) package ExomeDepth.

Answer 2

[geocarvalho]

I have been collecting some papers about CNV analysis (link). There is a topic about Whole Exome Sequencing (WES). Nowadays, I'm using Exomedepth+cnvScan. I'm also trying to add more callers to my pipeline.