Alignment of 1000 Genomes Project reads to reference assembly GRCh38

GigaScience
Xiangqun Zheng-Bradley1000 Genomes Project Consortium

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 a...Continue Reading

References

May 13, 2010·BMC Bioinformatics·Jessica SeverinJavier Herrero
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Jan 20, 2011·Genome Research·Markus Hsi-Yang FritzEwan Birney
Jul 14, 2011·PLoS Biology·Deanna M ChurchTim Hubbard
May 1, 2012·Nature Methods·Laura ClarkeUNKNOWN 1000 Genomes Project Consortium
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Oct 26, 2016·Journal of Human Genetics·Masahiro KanaiYukinori Okada

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Citations

May 18, 2019·Bioinformatics·Robert BuelsIan Holmes
Dec 16, 2018·Scientific Reports·Anna SupernatTomasz Stokowy
May 27, 2020·Genome Biology·Cristian GrozaGuillaume Bourque
Feb 6, 2020·Bioinformatics and Biology Insights·Eman Alzaid, Achraf El Allali
Mar 19, 2020·Wellcome Open Research·Ernesto Lowy-GallegoUNKNOWN 1000 Genomes Project Consortium
Dec 22, 2020·GigaScience·Samantha ZarateFritz J Sedlazeck
Jan 14, 2021·GigaScience·Taras K OleksykVolodymyr Smolanka
Feb 13, 2021·NAR Genomics and Bioinformatics·Wouter De CosterPeter De Rijk
Feb 26, 2021·The Journal of Molecular Diagnostics : JMD·Lisa A LansdonMidhat S Farooqi
Sep 28, 2021·PLoS Computational Biology·Manuel TognonLuca Pinello

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Methods Mentioned

BETA
exome sequencing
Illumina sequencing
PCR

Software Mentioned

bamUtil
cramtools
samtools
eHive
Shapeit2
ReseqTrack
HTSlib
FASTQ
bwakit
GATK

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