SNPs identification in Human

Question

[Javad]

Dear all,

I would like to ask you a question regarding identification of SNPs in individuals.

I have the exome sequence of around 20 individuals (Human) and I would like to identify the SNPs in the exome of theses persons.

I have never worked with SNPs before so I would be grateful if somebody can give me some hints regarding the identification of SNPs workflow so I can do some studies and I can find my way.

I am particularly interested to know the tools for SNPs identification and the standard workflow.

Thanks a lot,

Answer 1

[GenoMax]

GATK best practices page has comprehensive help for SNP calling. Look on the left side of the page for specific work flows (Germline, somatic, RNAseq). They gloss over alignments but I assume you are aware of how to get those done.