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Journal Article

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

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Timmermann,  Bernd
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Lowy-Gallego, E., Fairley, S., Zheng-Bradley, X., Ruffier, M., Clarke, L., Flicek, P., et al. (2019). Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project. Wellcome Open Research (open access publishing platform), 2019: 4:50. doi:10.12688/wellcomeopenres.15126.1.


Cite as: https://hdl.handle.net/21.11116/0000-0004-DA30-0
Abstract
We present biallelic SNVs called from 2,548 samples across 26 populationsfrom the 1000 Genomes Project, called directly on GRCh38. We believethis will be a useful reference resource for those using GRCh38,representing an improvement over the “lift-overs” of the 1000 GenomesProject data that have been available to date and providing a resourcenecessary for the full adoption of GRCh38 by the community. Here, wedescribe how the call set was created and provide benchmarking datadescribing how our call set compares to that produced by the final phase ofthe 1000 Genomes Project on GRCh37.