I am using pindel to detect long insertions, but it doesn't detect anything in any of my samples. However it detects inversions when I say to it not to put it. Why could be this? I called it in 250 samples where I know there are long insertions.
arctic monkeys do i wanna know concert
./pindel -f $ref -i $inputfile -o $output --report_interchromosomal_events false --report_duplications false --report_inversions false
is there any other software a part from breakdancer and pindel to detect long insertions?