Hello all,

I'm looking to create and examine haplotypes for specific variant sets from the 1000genomes dataset. All my variants are in chrX.

I downloaded the latest VCF for chrX from here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

In this file, I do not see any entries for most of my variants - even if they do have dbSNP entries that are sourced from the 1000genomes project. I do see these variants in my Phase 1 database.

Is it possible that the latest phase VCF does not contain all but some variants for chrX - as in, it's not complete yet? If that is the case, can I use Phase-1 calls? Can I go by this - http://www.1000genomes.org/faq/where-are-snps-xymitochondrial-chr/

I just want to make sure I'm not missing anything and that 1000genomes has indeed not made Phase-1 a part of Phase-3 release.