how to make LEGEND file for Reference Panels?
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15 months ago
nayeona.hi ▴ 50

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 • 548 views
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Entering edit mode
15 months ago

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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