VCF FILE OF DIABETES / HIV / MALARIA OF HUMAN POPULATION

Question

[Being Bioinformatician]

Respected members,

First question:

Do anyone have .fastq and .vcf file(with genotype) of human population (diseased and control set ) especially type 2 diabetes/Malaria/HIV. or if any link where I can download them for free.

I know about ncbi sra and ega but there again I have to write to corresponding authors. I am looking for one where I can download freely

Second question:

Can I use vcf file of 1000 genome phase 3 data for disease based study , i.e calculating dn/ds and Fst

Thanks in advance

[Michael]

Please don't invite to take the discussion off the board.

Answer 1

[Sean Davis]

For human data in SRA and ENA, you will very likely need to apply for access. There really isn't any way around it. In general, it is unusual to find human data that has been cleared for "truly public" consumption. The 1000Genomes data is one obvious and highly-utilized exception.

[Being Bioinformatician]

@sean I still have a doubt.. Can I use vcf file from 1000 genome only for inter-population comparative study (disease based ) of genes to check positive or negative selection

[Sean Davis]

I don't have an answer for you. Perhaps others can address help you with this one.