Detecting translocations on same chromosome

[abolia]

Hi Zev,

I am using WHAM to find translocations on my dataset and based on the description specified for WHAM, I see that you can only call a translocation on different chromosomes (basically by looking at the difference in CHROM and chr2 id). Is there a way WHAM can report translocations on the same chromosome?

Thanks for your help.

Ashini.

[Zev Kronenberg]

The breakpoints will be reported in the VCF file, however they might not have the "TRA" tag after classification. How big of intra-chomosomal events are you looking at? I might ignore the classification and look for large SV calls. If you have a set of known intra-chomosomal translocation you could create your own classifier dataset.

--Zev

[abolia]

Thanks Zev. This helps. I will look for the large SV calls.

Thanks,
Ashini