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vibansal / HapCUT2

software tools for haplotype assembly from sequence data
BSD 2-Clause "Simplified" License
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Haplotype blocks between chromosomes #100

Closed conchoecia closed 4 years ago

conchoecia commented 4 years ago

Hello, just wondering if HapCut2 can produce haplotype blocks that span scaffolds, or if the haplotype blocks are limited to within-scaffold relationships?

I am asking because I am working on detecting a chromosomal fusion relative to the reference with Hi-C data. Thanks! I don't think that HapCut2 does this, but I wanted to check with you to be sure.

vibansal commented 4 years ago

The haplotype blocks generated by HapCUT2 depend on the input data. For Hi-C, if there are reads linking distant sites on a chromosome, they will be linked together in a single block. I hope that answers your question.