how to import a 1000 genome project vcf file (chromosome file) into a mysql database
Hi All
I would like to import / upload a 1000 genome project vcf file (chromosome file) into a mysql database using sql.
If there are existing mysql dumps, please tell where I can find them.
Also if there is an official way-script I would love to see it
Thanks, pini.
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pinikoma •
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See Do People Import Vcf Files Into Databases?, Vcf Database Table Structure. But inserting a VCF into a database is a bad idea unless you want to expose your data. Tabix/Tribble indexes should do the job.
Meanwhile, Ensembl has stopped putting a lot of variation data into MySQL and instead are storing everything in VCFs (much more compact).