SNP simulation with SAM files

[YKay]

Hi all, I am trying to embed SNPs directly in a sam file for simulation purposes, i.e for a given set of genomic positions, to identify the reads the cover them and to overwrite values (nucleotides) on the positions on the reads that correspond to the input genomic positions.

Any ideas on how to do this ? in particular in R?

Thanks,
Yiannis

[swbarnes2]

Wouldn't' it be simpler to tweak your reference file, so that now it has discrepancies from your reads?

[YKay]

Thanks swbarnes2, this is good idea but it is not an option in my case. I am trying to simulate mixtures of populations (with different allele frequencies) and for this I need to construct reads for each component in the mixture.