I am really bad at manipulating sam files... I was looking for a simple way to count, within a sam, the number of indels <=2 nucleotides. I also want it to be position specific, which means for me that, for a single position, if I have a read coverage of 100 and in each read there is a deletion, I only want to count one.
Is this a simple thing to do using samtools or any other scripting method ?
Thanks for your help !