Translocation detection using SNP arrays or exome-seq (no cell lines).. ideas ?

[dickie_ho]

Hey seqanswers community

I am currently working on a CNV project using old data from illumina 610k arrays. I know this is almost impossible to detect translocation using a probe based method but would like any feedback i can get. I do have exome-sequencing and RNA-sequencing on a very small cohort of these samples and would like any feedback if people have attempted using exome-seq to determine translocations. (without finding the breakpoints I'm assuming its almost impossible to do)

The reason I ask is I do not have cell lines and have very little to none DNA left to do PCR to confirm a translocation exist.

Any input would be much appreciated

Thanks

Josh

[TiborNagy]

You can use splitread. It is a rather old program, but maybe can help you.

[dickie_ho]

Thanks TiborNagy

Will have a good look tomorrow ..

[dickie_ho]

Hey TiborNagy

Do you suggest finding the break points and lining that up with CNV information ??

Cheers

Josh