Convert Recombination txt file to Plink format
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2.4 years ago
nanodano ▴ 30

Hi everyone, I have a recombination map downloaded from the Broad Institute (https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/) that looks like this:

chr position COMBINED_rate(cM/Mb) Genetic_Map(cM)
55550 0.0000000000 0.000000000000000
1 632942 0.0000000000 0.000000000000000
1 633147 0.0000000000 0.000000000000000
1 785910 2.6858076690 0.410292036939447
1 788439 2.8222713027 0.417429561063975
1 788511 2.9813105581 0.417644215424158
1 792862 2.9806151254 0.430612871834774
1 794568 3.0780969498 0.435864105231133
1 805477 3.0751332930 0.469410734324470

I need to convert it to PLINK format, which looks like this:

1   .   0.000000    55550
1   .   0.080572    82571
1   .   0.092229    88169
1   .   0.439456    254996
1   .   1.478148    564598
1   .   1.478214    564621
1   .   1.480558    565433
1   .   1.488889    568322
1   .   1.489481    568527
1   .   1.931794    721290

Any recommendations on how to do this? Does anyone know if PLINK offers recombination maps for hg38 already?

Many thanks!

plink recombination map genetic • 451 views
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