Hello everyone,
I am working on a Python script to process SNP data from several sequenced samples. An important part of this is querying the results (through Chromosome, Position, Reference and Alteration) against a SNP database (I would love to work with dbSNP, 1k Genomes, HapMap and Cosmic), in order to check if they are registered and if they are somatic or germinal (I do not have any control sample).
Is there any established way? I have not found anything similar in BioPython, and I can only think of querying the sites and parsing the outputs, but...
As I said, I am working on a Python script, and it would be great to find a solution using Python, but of course I am opened to any other suggestion!! :)
Sorry for the doubt, but I am still learning the basics, and I swear I searched and could not find any guide! :)
Established way:
Thank you very much, indeed :)
Yes, oncotator uses Python (yay!). Just to ensure, using only oncotator would be perfectly valid, right?
Being curious, which one would you recommend, annovar or oncotator?
Once again, thank you!!
Hi,
Annovar is pretty well known and powerful tool for annotation. Whereas oncotator as in the name, specially designed for data relevant to cancer and has some special annotations relevent to cancer such as TCGA copy number, cancer gene census, etc. But if you have general data, Annovar is more than enough.