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Are some "Possible Deletion"s actually intra-contig rearrangements? #32

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nh13 opened this issue Dec 29, 2023 · 0 comments
Open

Are some "Possible Deletion"s actually intra-contig rearrangements? #32

nh13 opened this issue Dec 29, 2023 · 0 comments

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@nh13
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nh13 commented Dec 29, 2023

Looking at what falls through as a possible deletion, I think fgsv categorizes the following as a "possible deletion" when it's more likely a "intra-contig rearrangment":

  1. The left and right breakends have the same contig and strand
    2a. When they are both on the + strand, he position of the left breakend is greater than the right breakend
    2b. When they are both on the - strand, he position of the left breakend is lower than the right breakend

A deletion means the same contig and strand and jumping "forward" (5'->3').

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