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EichlerLab / pav

Phased assembly variant caller
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insertion and deletion from different chromosome #43

Closed chycheng2015 closed 11 months ago

chycheng2015 commented 1 year ago

Hi,

I tried to found SVs in a phased assembly genome of HG002, and found some insertion and deletion corresponding to ref (GRCh37) are from different chromosom. For example, an ins on chr1-34044-34045 are from paternal's chr12-21613-24633. How do you explain this?

paudano commented 1 year ago

It's hard to know without more specific details. 3 kbp is about the size of a human LINE, are you seeing a LINE insertion in one place and the absence of a reference LINE in another? Are the variants in segmental duplications. See what's at the locations in the UCSC browser (turn on "Segmental Dups", "RepeatMasker", and TRF tracks).