I have a list of a few hundred SNPs given by rs number. I want to get the chromosome and position for each SNP. For example:
duplicate of: How to get the chromosome physical position from rs numbers? , Get SNP position from a python interface.
I created an iOS app for this exact purpose, I welcome any feedback.
you can download this information from NCBS dbSNP site. On the other hand, you can also use the SNP-nexus site. Very useful.
Thanks I got it! http://www.ncbi.nlm.nih.gov/projects/SNP/dbSNP.cgi?list=rslist
SNP-nexus is quite good. However, when the rs number > 20000, it will become very slow...
BioMart. Help video here.
Use the variation dataset, short variation and indels. Then filter by rsID and choose the position as an attribute.
I have a data file for imputation only with rs numbers and my referecence vcf file has rsnumber:Chro:position:allele1:allele2.
Biomart has the H. sapiens variation in GRCh38 and my ref. file (1KG) is in GRCh37. How could I proceed?
Use the dedicated GRCh37 Ensembl site.