tool to detect large deletions

Question

[lait]

Hi,

I used to look for large deletions in IGV, but is anyone familiar with a tool that could detect large deletions, (for example, deletions of 4 exons in a certain gene) effectively and automatically ? any recommendations ?

edit: I am looking for those big deletions in around 300 genes only, so we don not need genome-wide deletion detection. we are doing whole exome sequencing for humans samples (Illumina hiseq 2500), this is done on a monthly bases, around 8 samples per month.

thanks.

[WouterDeCoster]

You tagged WES, so we'll have to assume you have whole exome sequencing data using short read sequencing? How many samples? Do you know what to look for or do you need genome-wide deletion detection?

Please try to be as complete as possible when asking questions.

[lait]

thanks, already edited the question.

Answer 1

[bari.ballew]

There are several major algorithms that are used to find large deletions (structural variants, or SVs). Most of them rely on a pair of sequencing reads spanning the breakpoints of the SV. If you have WGS data, the chance that you sequenced across the breakpoint is pretty good, but for WES data, it's much less likely that the breakpoint is in the sequenced region. So, you want to focus on SV calling tools that use read count (also referred to as read depth or coverage), and don't require spanning reads. Some read count-based tools that can handle WES data include EXCAVATOR, CoNIFER, and ExomeCNV. I would recommend using at least two different tools, as there tends to be a lot of noise when calling SVs, and looking at concordance between callers is one way to find the true signal.

Answer 2

[ATpoint]

There are many. lumpy, manta, pindel and others. The keyword is structural variant caller.