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fgvieira / ngsLD

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
GNU General Public License v2.0
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Example GL File #27

Closed gaxyz closed 2 years ago

gaxyz commented 2 years ago

Hello,

I am trying to run ngsLD, but I am having trouble figuring out the correct input format for genotype likelihoods. I tried beagle gzipped output and a modified version of it (for only one individual and four loci):

-1      0       0.333333        0.333333 

0       -1      0.458889        0.541111

0       2       0.000000        1.000000

-1      0       1.000000        0.000000

But it does not work (error:cannot read GZip GENO file. Check GENO file and number of sites!).

Could you please provide an example GL file?

Thanks!

gaston

fgvieira commented 2 years ago

You can check the description of the beagle format here.

gaxyz commented 2 years ago

Thanks for the prompt response. Just to be certain, it accepts beagle format as input?

fgvieira commented 2 years ago

yes, but is´t has to be gziped