1000 Genomes reference panels
Hi,
Could someone please advise on the 1000 Genomes reference panels? I saw that the European ancestry Phase 3 is built on GRCh37 (https://cncr.nl/research/magma/). Is there a way to do a lift over to GRCh38?
Thank you SB
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Arup Ghosh
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Shalini •
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Shalini •
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You can download the 1KG GRCh38 data from the EBI FTP server and subset it, then convert it to a MAGMA reference using PLINK. For more details, check the README file inside the reference data folders and the reference manual.
1KG GRCh38 SNV: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20181203_biallelic_SNV/
AWS Open data
aws s3 ls --no-sign-request s3://1000genomes/
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