Our final release of the Phase 3 variant set is now available on the FTP site, including a newly added VCF file for chrY.
The chrY variant calls were made with a different process from that of the autosomes; a separate README is available in the release directory describing some details.
The chrX VCF file has been updated to include standard annotation including DP, continental super-population allele frequency.
The site file in the release directory is now wgs containing autosomes, chrX and Y.
Two algorithms were used to discover short tandem repeats (STRs) in the phase3 data. However the STRs did not make into the final integrated call set. They are now available separately here.
The VCF files in the main release directory are also now available here in BCF format for faster processing time.
This release includes super population allele frequencies in the main release VCFs and functional annotation from the Ensembl Variant Effect Predictor along side many other datasets in the supporting directory. The complete list of data is covered in the Supporting Directory README. The issues which have been raised and resolved since our initial release are covered in the Known Issues README.
Please send any questions about this data set to info@1000genomes.org