I have a file of structural variation information of donor genome to hg19 reference genome. The information is like this:
17 1104685548616 assembly_comparison_inversion 5886015 5886567 . - . .
17 1104685270005 assembly_comparison_inversion 43210707 43211858 . + . .
17 1104685351393 assembly_comparison_inversion 58198056 58201613 . + . .
17 1104685350756 assembly_comparison_inversion 60646046 60646518 . + . .
the 7-th column indicate whether the SV event happend in positive strand or negative strand. As you can see this is inversion event, and I want to put these events back into hg19 reference genome to reconstruct donor genome.
What I do not understand is how could SV events just happend in one single strand? and how to locate the event site if it happened in negative strand?
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Chen Sun
1 answer
For flattened representations. you need to combine multiple lines in the BED file to reconstruct the full event. The BED file describes the identified breakpoints and then you combine these into the complex structural variation event. I found this review by Aaron Quinlan and Ira Hall super helpful for understanding the representations and different cases, especially figure 2:
http://faculty.virginia.edu/irahall/support/webpdfs/Characterizing_Tren_Gen2012.pdf
It took me a bit of practice to begin to see the events. My best suggestion is to draw out the breakpoints on paper until they become second nature. Hope this helps.
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