Are there any FASTA files containing 1000 Genomes variants or haplotypes?

We do not provide FASTA files annotated for 1000 Genomes variants. You can create such a file with a VCFtools Perl script called vcf-consensus.

An example set of command lines would be:

#Extract the region and individual of interest from the VCF file you want to produce the consensus from
tabix -h 17:1471000-1472000 | perl vcf-subset -c HG00098 | bgzip -c > HG00098.vcf.gz

#Index the new VCF file so it can be used by vcf-consensus
tabix -p vcf HG00098.vcf.gz

#Run vcf-consensus
cat ref.fa | vcf-consensus HG00098.vcf.gz > HG00098.fa

You can get more support for VCFtools on their help mailing list.

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