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zeeev / wham

Structural variant detection and association testing
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Detecting translocations on same chromosome #21

Closed abolia closed 8 years ago

abolia commented 8 years ago

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.

zeeev commented 8 years ago

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 commented 8 years ago

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

Thanks, Ashini