How to insert dbSNP in a database?

Question

[magnolia]

Hi everyone,

I want to insert the whole dbSNP VCF files (both grch37 and 38) into database. Postgres, or MySQL.

Has anyone done this?

How do you deal with the size of the table?

All in one table or partition it?

If partitioned, how do you query?

Thank you in advance!

Answer 1

[Pierre Lindenbaum]

1) why do you need this ?

2) you can always upload the UCSC dbsnp files. ex.:

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/snp150.sql

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/snp150.txt.gz

3) see also: Do People Import Vcf Files Into Databases? ; what sql schema to store a vcf file ? ; Vcf Database Table Structure ; ...

[magnolia]

Thank you!

1) I need this because I want to connect all the data I need query via SQL.

2) Thanks a lot but this file only has 200 million rows whereas dbSNP VCF has more than 1 billion rows. Why is that?

[Pierre Lindenbaum]

2) not the same version of dbsnp, not the same build

[magnolia]

Oh so, there is 800 million rsid difference between 150 and 155? That's very interesting. Also another reason that I had to create a db table from VCF.