Is there a way to get the size of INDELS in Rsamtools similar to the output of samtools mpileup where for instance the G -> GAG insertion is printed as +2AG for each occurence (i.e. read-wise) I failed to find a solution with Rsamtools::pileup(), the tabular output looses the per-read information. Is it possible by other functions in Rsamtools, perhaps via Rsamtools::scanBam() somehow by parsing the CIGAR together with start and end positions ? Thanks

Mads Heilskov