Using dbsnps or use samtools to call from 1000 genomes

[southan]

Hi all,

I am going to get snps in chr1 on 1000 genomes (latest).
Do you think I should use dbsnp132 or I should use samtools to call snps again from bam files on 1000 genomes?

Thank you very much.

[laura]

You could use tabix to get the snps from our most recent release of snps

There are instructions here

http://www.1000genomes.org/faq/how-do-i-get-sub-section-vcf-file

Our most recent release is

ftp://ftp.1000genomes.ebi.ac.uk/vol1...hase1_release/

[southan]

Thank Laura!

I downloaded one chromosome of SNPs on the website.

I am using VCFtools to extract individuals but it takes a lot of time to get each individuals (22 samples in two days).

Do you think VCFtools is suitable for extracting many samples?

[laura]

What are you actually trying to achieve?

Is there a reason you need a vcf per sample?

Which bit of vcftools are you using?

[southan]

Thank Laura,

It's Ok now.

I used:
1/ tabix to get some regions from chr1.
2/ Vcf-subset to get samples from the regions.