how to make LEGEND file for Reference Panels?

Question

[nayeona.hi]

Hi, I am a beginner and in the work of pre-phasing for gwas data with 1KG reference.
Now I am doing generating haps and sample files of 1KG data via shapeit but cannot find making LEGEND files.
How can I get legend files?
OR, is it possible to make txt file consisting of id / position / allele A / allele B from map file?

[anahit]

Hi, where can I find legend and hap files for 38 build? I am trying to use vcf2impute_legend_haps script provided by IMPUTE2, but it does not give me any results with vcf files downloaded from here http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/

Thank you!

[Paravee]

Not sure if you've already found an answer or not, but I think PLINK can convert vcf files to hap and legend format.

Answer 1

[Kevin Blighe]

These and other files are available from here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html

Also, see my pre-phasing and imputation pipeline by following these posts:

• C: Phasing with SHAPEIT

Kevin