Question: odd size of breakdancer INV
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gravatar for kirill1984
6 months ago by
kirill19840
kirill19840 wrote:

Hi guys,

I called structural variants with breakdancer-1.0_2010_06_24.
I have troubles interpreting output for inversions:

Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib Allele_frequency

Chr 125880948 6+12- Chr1 25881746 6+12- INV -145 99 9 lab|9 0.0625
Chr1 25932635 20+0- Chr1 25932884 13+11- INV 39 73 4 lab|4 0.173913
Chr1 25933315 9+11- Chr1 25933631 0+19- INV 125 38 2 lab|2 0.166667
Chr1 26473552 13+0- Chr1 26509031 14+0- INV 35397 99 13 lab|13 0.245283
Chr1 26507577 0+19- Chr1 26509719 0+18- INV 2201 99 18 lab|18 0.166667
Chr1 28971112 14+17- Chr1 28971891 14+17- INV -235 99 11 lab|11 0.289474

As you see, INV size (in bold) is negative at first and last row. I saw such things many times.

I'm wondering if anyone can explain why is that?

Thanks!

ADD COMMENTlink written 6 months ago by kirill19840
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