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Free keywords:
alignment; reference genome; GRCh38; sequence reads; read mapping
Abstract:
The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples
in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased
variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late
2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is
possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone
process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not
see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38.
Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall
the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have
finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold–aware BWA-MEM. The
resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released
on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the
primary sequences and alternative contigs of GRCh38.
