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Hello-I'm new to all this so first and for most please forgive my ignorance.
Secondly, after creating a SNP report with DNAstar's SeqManPro (NGS project with Illumina data)I noticed that the contig position and the reference position didn't match, they were significantly off actually. So my question is that if there is enough depth and SNP % then that is enough to call it? I thought that the contig and the ref should line up at positions where the SNP is, otherwise how could we be sure where the SNP is being called and that it is actually a SNP???
PLease anyone that can clear this up for me would be great. As I'm a rush job, self taught, what did I get myself into, thesis masters student, just trying to graduate!!!!!
Crystal
Secondly, after creating a SNP report with DNAstar's SeqManPro (NGS project with Illumina data)I noticed that the contig position and the reference position didn't match, they were significantly off actually. So my question is that if there is enough depth and SNP % then that is enough to call it? I thought that the contig and the ref should line up at positions where the SNP is, otherwise how could we be sure where the SNP is being called and that it is actually a SNP???
PLease anyone that can clear this up for me would be great. As I'm a rush job, self taught, what did I get myself into, thesis masters student, just trying to graduate!!!!!
Crystal