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how to make LEGEND file for Reference Panels?

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?

legend file shapeit pre-phasing imputation
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updated by Paravee • Paravee • written by nayeona.hi nayeona.hi

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

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written by Paravee • Paravee

1 answer

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:

Kevin

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written by Kevin Blighe Kevin Blighe

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