SVDetect Intrachromosomal Deletion

modi2020

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Join Date: May 2012

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SVDetect Intrachromosomal Deletion

01-01-2015, 09:43 AM

Hi Guys,

I ran SVDetect on Next generation paired end data and got the output but I am confused as to how to interpret the intrachromosomal deletions.
My understanding of the basic deletion meaning is that a part of a chromosome is deleted. However SVDetect gives two coordinates for the deletion position which is confusing to me. Can anyone explain this for me please?

I will give the header and an example of a deletion below:

In this example SVDetect detected a deletion in chromosome 15 apparently at 8996748-8997144 but then it mentions that it was also in the same chromosome at 8997145-8997470.

Header:

chr_type SV_type BAL_type chromosome1 start1-end1 average_dist chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering final_score breakpoint1_start1-end1 breakpoint2_start2-end2

Deletion:

INTRA DELETION UNBAL chr15 8996748-8997144 416 chr15 8997145-8997470 19 100% 100% 100% 1 8997144-8997130 8997089-8997146

I would greatly appreciate your help as I am trying to wrap up this project now.
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