Which 1000 genomes 30x files should I use for imputation?

Question

[Apprentice]

I would like to do an imputation using data of 1000 genomes phase 3 30x (GRCh38) as a reference panel. 1000 genomes phase 3 30x data seems to be available in various versions. Which file should I use for the imputation? For example, I am thinking of using a file that can be obtained from the following URL: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/

Answer 1

[4galaxy77]

Yes, the vcf files are what you want if you need to use them as an imputation reference. Those files plus the indexes are correct. You may need/want to change the format dependent on what software you are using (e.g. convert to bref format if beagle5), but the software should explain. The VCFs are fine for use with shapeit4.

[Apprentice]

Thank you for your comment.

There are several types of genotype data for 1000 genomes phase 3. For example, I found the following two types of data. http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/ http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_raw_GT_with_annot/

Which of these should I use for imputation? Or are there other data more suitable for imputation? If you know, I would appreciate it if you could let me know.

[David-walson]

Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it properly. I would appreciate if you could offer me some advice. Looking forward to your supply! Wish you a good day.