I have some RNA Seq data (whole genome) from different strains and I'm looking for SNPs inside.
In some exons I have a good coverage (nucleotide are mapped 1500 times) but in other positions I have low coverage ( 5-10-30 for example)
Do you know which is the minimum value to consider a SNP as a good candidate?
I mean, if I have a SNP in the mutated strain compared to wild type and in that position I have 1000 reads mapping, I can trust it, but if in an other position I have only 15 reads mapping there, can I consider it too? or the reads are too less?
Do you know any papers about this?
Thanks in advance.