Hi everyone,
here I am working on an evaluation of queries on variants and genotypes which needs me to import the tested vcf files into sql database. I am using MySQL and PhpMyAdmin to accomplish it but I am just a beginner.
My questions are:
If I have a .vcf file, how can I convert it into .csv? With python or can be done in vcftools and how?(I consider it's the most accessible way to import it in MySQL later)
How can I get the list of individuals and all variants that they correspond to?
I know that vcftools can filter the variants of a specific individual/sample, but what if I want the whole sample list in 1000genomes in order to create a table assigning individual to their variants, and another table assigning metadata about each variant ( I think these information equals those in a vcf file.)
Your help will be very appreciated.
•
written
by
feng9oly •
1 answer
I've written a VCF to sql : https://github.com/lindenb/jvarkit/wiki/VCF2SQL
see also:
•
written
by
Pierre Lindenbaum
Log in to answer this question.
-
False negatives -Hard filtering
written by priya.bmg •
-
How to create a database of genetic variants from multiple annotated VCFs and variants found in the…
written by aleksmllr •
-
Conversion of the vcf file of structural variants in bed format
written by Myosotis1979 •
-
Filtering by specific genotype VCF
written by virpatel3 •
-
Does vcftools or GATK have an option to skip indels when making alternate sequence?
written by severalorks
-
Using VCFtools to obtain fasta files
written by severalorks
-
Using VCFtools to find which population codes individuals in a vcf file belong to
written by severalorks
-
how to import a 1000 genome project vcf file (chromosome file) into a mysql database
written by pinikoma •
-
Vcf File With Variants And Genotypes For A "Single Individual"
written by Nasrin •
-
1000 Genomes Individual Genotype Data
written by win
Hi,
how should your mysql datatable look like?
As in the vcf file the columns are tab-seperated you allready have a format you can import via phpmyadmin. But if you want to spilt the several fields in the INFO column, more work is needed.
fin swimmer
Thank you for asking. I want to make a datatable to combine individual id and variant id, type of instance. But now I am actually feeling confused because as far as I am concerned, in a VCF there are many variants assigning to an individual, so these two column are not 1-to-1 so it could be strange to arrange the structure.
Now I have imported some data via phpmyadmin and I thought in order to access to more queries I also need to spilt the fields in the INFO column.