We have produced an extended integrated and phased biallelic SNV and INDEL call set. This uses the same input data sets as our biallelic SNV call set but now includes INDELs in the creation of the phased call set.
The files include: per chromosome files with genotypes for all samples, a genome wide sites file and genotype files for each of the supporting call sets. The main files contain only unrelated individuals, with details for related individuals available in a separate set of files. Data files are available at: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/
A data note describing the biallelic SNV set is now available at Wellcome Open Research.
We will work toward making details of the SNV and INDEL data set available as soon as possible. The data is in the process of being submitted to EVA.
Please contact info@1000genomes.org with any questions.