Entering edit mode
6.8 years ago
athena (˚▽˚)
•
0
Hi all,
After running the breakdancer_max function with parameter -t (as in example pipeline), which is supposed to detect only inter-chromosomal translocations (CTX), I get a non-negligible amount of structural variants that are not CTX.
Something similar was posted here 5 years ago
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads
chr1 32470399 3+3- chr1 32470448 3+3- CTX -334 38 3
chr1 48881618 6+6- chr1 48881638 6+6- CTX -334 66 6
chr1 88289457 0+7- chr1 88289522 0+7- CTX -334 51 7
chr1 123356883 3+3- chr1 123356893 3+3- CTX -334 58 3
chr1 16008305 27+0- chr1 192660464 0+35- CTX -334 99 31
chr1 58613994 0+21- chr2 22739547 21+0- CTX -334 99 21
chr2 49607944 6+0- chr2 49607980 6+0- CTX -334 42 3
chr2 5379438 51+189- chr2 73012734 51+189- CTX -334 99 240
chr1 88295101 11+0- chr2 92791560 0+11- CTX -334 99 11
chr2 98664984 11+5- chr2 98665149 11+5- CTX -334 70 8
chr2 100315656 2+2- chr2 100315674 2+2- CTX -334 31 2
chr1 16008305 7+0- chr2 153793874 0+5- CTX -334 42 5
chr1 119990532 8+6- chr2 163292624 6+8- CTX -334 99 14
chr1 40738568 15+0- chr2 181917252 2+13- CTX -334 99 13
chr1 95452110 115+0- chr2 181917252 0+78- CTX -334 99 78
chr1 95452294 78+1- chr2 181917252 0+54- CTX -334 99 54
chr1 95452110 0+5- chr2 181916190 5+0- CTX -334 43 5
chr1 103185502 0+4- chr3 3160503 0+4- CTX -334 50 4
Any ideas why this could be the case?
