Question

VCF FILE OF DIABETES / HIV / MALARIA OF HUMAN POPULATION

1

Entering edit mode

9.5 years ago

Being Bioinformatician ▴ 250

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

SNP next-gen RNA-seq • 2.4k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by Being Bioinformatician ▴ 250

0

Entering edit mode

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

ADD REPLY • link 9.5 years ago by Michael 55k

Ram · Answer 1 · 2015-06-14

0

Entering edit mode

9.5 years ago

Sean Davis 27k

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.

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by Sean Davis 27k

0

Entering edit mode

@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

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by Being Bioinformatician ▴ 250

0

Entering edit mode

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

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by Sean Davis 27k