1000G Reference Panel Hg38 Michigan Imputation Server

Question

[yvyu]

Hello,

I am trying to align my data with the 1000G data set, and my data is aligned under the hg38 build. I am unable to find a reference panel that would align under the "perl cmd" for this website (https://www.chg.ox.ac.uk/~wrayner/tools/), and I only find the hg37 build. Is there one that is readily available or do I have to compute my own? Although the website does have a hg38 version, under the TOPMed Reference panel, I ideally want to utilize the 1000G Reference list.

[bk11]

Performing pre-imputation QC of your data using hg38 TOPMed Reference Panel and later using 1KG reference (hg38) for imputation in Michigan Imputation Server should not be any problem.

[yvyu]

I will look into this. Thank you.

Answer 1

[Raony Guimarães]

Here is a phased panel for the 1000Genomes using hg38

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/

or

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/