Breakdancer parameter -t labels non-CTX events as CTX
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4.5 years ago

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?

breakdancer translocation • 929 views
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