Identify point mutations from each read in bam files and change to N

Question

[sam]

Hi All,

Is there a way around reading a bam file to change the mutated base to 'N' in the bam file?

Thanks!

[Pierre Lindenbaum]

why ? what are you trying to do ?

[sam]

I have short-read data for a cultivar and want to generate assembly for the genic region based on a reference genome. Apart from the uniquely mapped reads, I am also using filtered multi-mapped reads (to improve coverage) with a certain number of mutations in these reads. However, I want to substitute the mismatched base in the muti-mapped read against reference to 'N'.