I just started working with VCF files and would like to use the data of the 1000 Genome project. I found that the most recent version can be downloaded at ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . For my functional analysis, I need the position of every exon borders. Therefore I am looking 1) for the FASTA file, which was used as a reference during SNP calling and 2) a corresponding GTF file for annotation.
1) For the FASTA files, it is stated within the VCF files, that it comes from here: ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
However other post of Biostar propose using the following, which is a little bit larger: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
2) For the GTF files, I'm not sure if there even is one to download.