Can hapdup preserve inter-chromosomal heterozygous translocations?

[riyasj327]

Greetings,

Thank you so much for this amazing tool!

I have been using Hapdup to convert my nanopore flye assembly to diploid. I noticed that one of the interchromosomal translocation is getting missed in the diploid assembly. I see that the reads with translocation are getting utilized by flye even though I do not see the translocation in the haploid assembly. But it should be captured in the diploid assembly? I see that reads with the translocation are not present in the filtered bam and then when I check the margin haplotagged bam, I see both haplotypes are normal (without TRA) based on the read haplotype allocation. So, just wanted to check if the algorithm itself doesn't support inter-chromosomal translocations at the moment? Are the reads with the TRA is getting filtered in the first step of filtering alignment itself as I suspect?

Any thoughts on this would be really helpful!

thanks,
Riya

[mikolmogorov]

Hi Riya,

Yes, Hapdup currently only supports inversions, but not interhromosomal translocations, unfortunately. Hapdup was really developed for "healthy" human genome in mind, so inter-chromosomal SVs are unexpected.

[riyasj327]

I see. Thank you so much for you reply! @mikolmogorov