[Help needed] Translocation detection excluding telomere and repeated sequence

[ThDef]

Hi,

We are currently trying to detect translocations between one of our custom genome and ONT data but we are facing some troubles as the number of detected translocations are way higher than anticipated. After analyzing a subset of reported BND SV, we found out that quite an amount of them were repeated sequence and telomere shared across 2 or more chromosomes. Is there a way to filter those through the parameters to show only SV from reads where it is detected that the sequence presents the following pattern :

Unique Sequence from Chr A // Breakpoint // Unique Sequence from Chr B

and not

Shared Sequence from Chr A & B // Unique Sequence from Chr B

I don't know if my issue is clear, sorry if not

Thanks for your help,

[CoREse]

Hi, ThDef,

I am afraid that there is currently no such mechanism that can realise your filtering purpose. But you can try the -include_bed THISBEDONLY.bed parameter to indicate the areas where you want to detect SVs and exclude the telomere areas.

Best wishes,
CRE