I would like to simulate the dna-seq paired end data with common sequencing errors and snps (diploid organism).
But I do not want to do it on entire fasta file. I have already generated the fragments (300-500bp) using certain protocol. Now I want to generate paired end data from a set of fragments i.e read the fragment from both the ends and include error profile and SNPs so that I can validate the SNP caller I'm interested in.
I would like to know if there is any easier way to do it. Otherwise I need to spend lot of time in writing it from scratch.