Hi, I just ran breakDancer on a bam file. The program ran for a while, but gave out nothing in its input.
The configure file (manually configured as described on its website) is:
map:my.bam mean:334 std:44 readlen:
100.00 sample:mySample exe:samtools view
I then used the following commands to call inter-chromosomal translocation:
breakdancer_max -t -q 20 -r 10 config > result.txt
However, after several hours, the program quit without notifying anything, and the result.txt is just like:
#Software: BreakDancerMax-1.1r112
#Command: breakdancer_max -t -q 20 -r 10 config
#Library Statistics:
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib recal.bam
It didn't give any output except for the headers. Do you have any experience with it? Thank you very much
The configure file (manually configured as described on its website) is:
map:my.bam mean:334 std:44 readlen:
100.00 sample:mySample exe:samtools view
I then used the following commands to call inter-chromosomal translocation:
breakdancer_max -t -q 20 -r 10 config > result.txt
However, after several hours, the program quit without notifying anything, and the result.txt is just like:
#Software: BreakDancerMax-1.1r112
#Command: breakdancer_max -t -q 20 -r 10 config
#Library Statistics:
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib recal.bam
It didn't give any output except for the headers. Do you have any experience with it? Thank you very much
Comment