Working with 1000G data files

Question

[goodcow]

I'm trying to work with files downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521

What tools do I need to work with these files? I believe it is vcftools and tabix, right? The documentation is not clear at all.

[Bert Overduin]

Maybe you could explain what you're trying to achieve? "Working with files" sounds very vague.

[Giovanni M Dall'Olio]

it depends on what you want to do. VCFtools will be good for most things.

[goodcow]

Do I have to unzip the .vcf file before using vcftools?

Answer 1

[1234Jc4321]

http://www.1000genomes.org/using-1000-genomes-data

look at the file intitle "The 1000 Genomes Tools"

It's pretty clear.

[goodcow]

I'm going to be working with SNPs. To clarify, this index has the SNP files, correct? ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/

[1234Jc4321]

yes. like Phillip told you in your other post.

[goodcow]

Does the .ALL.wgs...vcf.gz contain ALL the SNPs? If so, what's the point of the .ALL.chr1, chr2, ... chrX.vcf.gz files? I think that's what I really don't understand. Thanks for your help.

[Bert Overduin]

As you can see from the names, the file

ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz

only contains the variant sites, whereas the files

ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz

etc.

contain all the genotypes for the 1000 Genomes individuals.