Update June 6 2019: Changing data repository links to EBI ftp site, which works with up-to-date build of git-annex from http://source.git-annex.branchable.com as of June 3 2019. Note that git-annex had ftp data sources disabled for some time between early 2018 and June 2019.
This directory contains the following files:
25 files with names of the format '1KGP_chrnn.vcf.gz', each of which should connect to the gzipped .vcf file containing 1000 Genome Project sequence variation files for the appropriate chromosome or mitochondrial DNA, hosted at the European Bioinformatics Institute.
4 files in the sub-directory scripts:
1000genomes_table.txt: Text file containing the SQL create statement used to generate a table for containing .vcf data. Has been used only in MySQL.
1000genomes_vcf_read.pl: perl script that retrieves a zipped .vcf file, unzips it locally, and reads headers and a couple of summaries of the contents of the file body into the table specified above.
1000genomes_output_json.pl: perl script that reads from that table and writes DATS-format 1KGP JSON files as uploaded to conp-dataset/metadata/example on April 1 2019.
1000genomes_validate_json.pl: perl script that validates user-specified JSON files against a user-specified schema, which has been used to validate all the 1KGP JSON files against the DATS dataset_schema.json.