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Working with 1000G data files

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.

1000genomes vcftools tabix
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updated by Ram Ram • written by goodcow • goodcow

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

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written by Bert Overduin Bert Overduin

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

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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

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written by goodcow • goodcow

1 answer

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

look at the file intitle "The 1000 Genomes Tools"

It's pretty clear.

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written by 1234Jc4321 1234Jc4321

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.

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updated by Ram Ram • written by goodcow • goodcow

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.

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updated by Ram Ram • written by Bert Overduin Bert Overduin

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