I have Illumina reads and a reference genome. I aligned reads to the genome and I have .bam and .sam files. I want the list of the mismatches of the reads with the reference genome but if one mismatch happened in multiple reads, I want it to be reported only once. For example if two reads have the mismatch of A->G on position 1000 of the reference genome, I want something like this:
I want the output file to be something like this:
Mismatch,Position,Frequency G,1000,2 A,3278,7 G,78732,5 T,89783,8 C,87494,8 A,13732,5 ...
Is there any tool available for doing that?