I have a config file out of Breakdancer that looks like below:
readgroup:transl_RG platform:illumina map:transl_RG.sorted.bam readlen:70.00 lib:transl_RG num:10001 lower:8.44 upper:996.38 mean:499.94 std:49.40 SWnormality:-2.61 flag:18(99.97%)32(0.03%)20006 exe:samtools view
I have put simulated translocations in the file and yet the breakdancer-max program does not identify any.
My command looks like this
breakdancer/bin/breakdancer-max -t -q 10 transl_RG.cfg > transl_RG.ctx
Has it something to do with the flags in the config file?
Do I need reads with the unmapped flag in order for Breakdancer to detect it.
Many thanks for your time.