CNV and Ion Torrent

[PandoraMid]

Hi! I work with Ion Torrent for detect some mutations in 2 specific genes: BRCA1 and BRCA2 (so I sequence just these regions), but the problem of this sequencer/software is that there's no way to detect some macro-deletion or macro-rearrangement in general (or if there's I don't know).

My question is: there's some software that start with a BAM file (or other output from Ion) and can detect this macro-rearrangement?

Thank you

[tristan dubos]

Hi , i m working in BRCA 1 and 2 too !! What do you mean about macro-rearrangement ? Big INDEL ?

[PandoraMid]

Yes, in particular macro-deletion!

[tristan dubos]

Witch variant caller do you use ? And witch part of BRCA are you exterminating (only Exon) ?

[PandoraMid]

Exon and junction Introd and exon

[tristan dubos]

An what is your pipeline actually ? do you find SNP and INDEL ?

[PandoraMid]

The software already reads snp and small indel, my problem is with exon's deletion. So i ask if one of you use a particular software for detect this "deletion of one or more exon" just in this two genes. I sequence just exon and junction intron-exon of this two genes.

[tristan dubos]

I understood your point. I didn't use a particular software for that because like you we looked only after SNP and small INDEL only for the moment. But we can detect deletion of exon if we looked in the depth coverage in the data control part when we check the run of sequencing.