Entering edit mode
Dear Rsamtools,
I'm hoping to use the pileup
function to output a table like the below. My goal is to be strand sensitive, distiguish +/- (for paired-end), include indels, as well count of 5'starts and 3'stops. I have so far been unsuccessful coming up with an implementation of PileupParam
to retrieve this information. Are you able to help? Thanks!
chr loc ref strand A T C G a t c g Insertion Deletion Stops Starts
1 888659 T + 0 9 0 2 0 0 0 0 2:AG|1:AGAG 1:ATT 3 2