I want to read in a BAM-file into R using the readAligned function from the ShortRead-package. However, I am just interested in the junction reads without indels and would like to filter using the CIGAR string for reads just containing M & Ns. How is that possible? I am just aware of the ScanBam argument "simpleCigar", which is not sufficient.
library("ShortRead") param <- ScanBamParam(simpleCigar=F)
.. reads in fully aligned reads and junction reads.. I would need a filter for reading in junction reads without indels
Thanks for helping me out!!