1000 Genomes 2504 phase 3 panel sequenced to high coverage

This README refers to 30x Illumina NovaSeq sequencing of 2504 samples from the 1000 Genomes project phase 3 sample set. These data were generated at the New York Genome Center with funds provided by NHGRI Grant 3UM1HG008901-03S1. Please email service@nygenome.org with questions or interest in undertaking collaborative analysis of this dataset. All cell lines were obtained from the Coriell Institute for Medical Research and were consented for full public release of genomic data. Please see Coriell (https://www.coriell.org) for more information about specific cell lines. The following cell lines/DNA samples were obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research: [NA06984, NA06985, NA06986, NA06989, NA06994, NA07000, NA07037, NA07048, NA07051, NA07056, NA07347, NA07357, NA10847, NA10851, NA11829, NA11830, NA11831, NA11832, NA11840, NA11843, NA11881, NA11892, NA11893, NA11894, NA11918, NA11919, NA11920, NA11930. NA11931, NA11932, NA11933, NA11992, NA11994, NA11995, NA12003, NA12004, NA12005, NA12006, NA12043, NA12044, NA12045, NA12046, NA12058, NA12144, NA12154, NA12155, NA12156, NA12234, NA12249, NA12272, NA12273, NA12275, NA12282, NA12283, NA12286, NA12287, NA12340, NA12341, NA12342, NA12347, NA12348, NA12383, NA12399, NA12400, NA12413,, NA12414, NA12489, NA12546, NA12716, NA12717, NA12718, NA12748, NA12749, NA12750, NA12751, NA12760, NA12761, NA12762, NA12763, NA12775, NA12776, NA12777, NA12778, NA12812, NA12813, NA12814, NA12815, NA12827, NA12828, NA12829, NA12830, NA12842, NA12843, NA12872, NA12873, NA12874, NA12878, NA12889, NA12890].

The sequence data is available in ENA and a listing of files, with metadata, is available in the accompanyiing index.

Analysis

Analysis work is being done by a number of groups, working toward variant calling, including identification of structural variation.

Initial analysis has been done by NYGC, including aligning the data to GRCh38, creating the CRAMs in ENA. The document NYGC_b38_pipeline_description.pdf contains a description of that analysis work and details of the alignment pipeline.

Should you have questions about this data please contact info@1000genomes.org