1KG SNPs and Indels file

[mpiro]

Greetings,

Is there any place to download 1000 genome SNPs and Indels data in a single merged file for each pilot (pilot 1 , 2 , and 3) ?
I am trying to use GATK and thought to use 1KG indels and SNPs vcf files to recalibrate my calls.

I apprecite your input.

[mpiro]

found them here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1..._data/release/

[pirooz]

I have the same question but I can't figure out which files to use. There are many folders and looks confusing to me.

Can you or someone please explain which files to use?

Thanks in advance.

.

[Michael.James.Clark]

found them here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1..._data/release/

You can just download all the Phase 1 data already merged from them. Check the 1000genomes.org site and the December update.

pirooz, there's a README in with the Phase 1 release from December that explains what everything is.

[pirooz]

Thanks Michael ... appreciate your comment.