Snp Discovery Requirement

Question

[Haluk]

Hi,

what are the essential requirements for the SNP discovery?

I would like to conduct a proof of concept research in order to be familiar with the similar future research by using some public access data out there. For example, do I have to use assembled or mapped sequence?

Is there anybody out there who would be able to suggest me any guideline?

Thanks.

[Sean Davis]

What is your starting point? What organism? By SNP discovery, what do you mean? A little more detail is needed to get the context.

[Sean Davis]

What type of data do you want to find SNPs in? Are your data going to be next-gen sequencing data or something else?

[Haluk]

I'm trying to find new SNPs other than referenced in dbSNP. At this point, I want to work on reference human genome if I can find its data on web, to find known SNPs that annotated in dbSNP.

[Haluk]

I wasn't be able to find any real data so far. If I can, NGS would be great.

Answer 1

[Sean Davis]

Data for the 1000 Genomes project are here. Then, have a look at samtools for manipulating the BAM files. You'll probably want to do a significant amount of reading the literature to get up-to-speed.