Alignment of 1000 Genomes Project reads to reference assembly GRCh38

Area of Science:

• Genomics
• Bioinformatics
• Human Genetics

Background:

• The 1000 Genomes Project generated extensive sequence data and variant calls on the GRCh37 human reference genome.
• A new human reference genome assembly, GRCh38, was released, necessitating an update for existing genomic datasets.
• Directly lifting variant coordinates from GRCh37 to GRCh38 is prone to errors, especially in repetitive regions or newly added genomic areas.

Purpose of the Study:

• To create high-quality sequence alignments of the 1000 Genomes Project data on the GRCh38 human reference genome.
• To provide researchers with accurate variant data compatible with the latest human genome assembly.
• To establish a foundation for improved variant calling and discovery using the GRCh38 assembly.

Main Methods:

• Sequence reads from the 1000 Genomes Project were remapped to the GRCh38 reference genome.
• Alternative scaffold-aware BWA-MEM was utilized for accurate read alignment.
• Sequence alignments were generated and stored in the CRAM format, a reference-based compression format.

Main Results:

• All 1000 Genomes Project sequence reads have been successfully remapped to GRCh38.
• High-quality sequence alignments in CRAM format are now publicly available.
• The remapped data are accessible via FTP and the European Nucleotide Archive.

Conclusions:

• Remapping sequence reads to GRCh38 is the optimal strategy for generating high-quality variant data.
• The released GRCh38 alignments enable enhanced variant discovery on the primary and alternative sequences of the latest human genome assembly.
• This work facilitates future genomic research by providing up-to-date and accurate genomic data.