Running beagle 5.0 Refined-IBD with no map file gives an empty output
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3.5 years ago
wz • 0

Hi all,

Did anyone tried to run IBD detection using the stand-alone program refined-IBD implemented in beagle 5.0?

I am running it without a genetic map file, which in the documentation, is acceptable.

"If no genetic map is specified, Refined IBD will assume a constant recombination rate of 1 cM per Mb."

But I always end up with an empty *.ibd.gz and *.hbd.gz output, and from the log file it looks like the program was running properly and gives no error message.

Here is the code I used for IBD detection and without a map file or other arguments. And I used the example input file provided by beagle as my gt input.

java -jar refined-ibd.16May19.ad5.jar gt=test.refined-ibd.16May19.ad5.vcf.gz  out=out

And if I added the map file provided and included the argument map=test.refined-ibd.16May19.ad5.map in the code, then the ibd and hbd output will have content in it.

I tried to search for the answer online, but I got an impression that most people are using beagle 5.0 for phasing their data, and less are working on IBD detection. So can someone tell me why is the reason, and how to fix it if I still wanna continue the job detecting IBD without a genetic map? Thanks in advance!

Beagle refined-IBD phasing • 1.4k views
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Hi, did you solve your problem? I faced the same issue here. I am working on non model species, so I am not sure whether I should produce a hypothetical map file or try another program. Thanks

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