Problem parsing beagle file

[tristanpwdennis]

Problem parsing beagle file

[populationgenetics]

Hi Tristan.

For some reason I cannot open your attached data. So there may be an issue with the files being corrupted somehow. However, if this is not the case then I am noticing that according to the output you have data from 314 individuals but only 632 columns in your beagle file. This is problematic because in a beagle file there are three columns with info about the markers followed by 3 columns per individual. So there should be more than 632 columns in your beagle file if there are indeed data from 314 individuals. Can I get you to tell me how many columns and lines the beagle file contains? And how many lines the freq file contains? Or perhaps send me the files without tar.gz-ing them?

Best,
Ida

[tristanpwdennis]

Hi Ida,
Thank you for your speedy reply!
I have counted the number of columns in the beagle file and it appears correct - there are 945 columns, which corresponds to 314 individuals + the 3 info fields. The freq and beagle contain 100 sites (a subsample). I have attached the files in question as a zipped folder - let me know if you have any trouble opening them again and I could email them to you?

Also, I notice that if I extract the first two individuals of data (so the first 9 rows), LocalNGSRelate appears to run fine. The BEAGLE file was generated with ANGSD 0.922.

Thanks again
Tristan

example_data_forlocalngsrelate.zip

[idamoltke]

Hi Tristan.

Apologies for the slow reply. My little 11 month old daughter and I have been have been sick the past week. However, I finally managed to take a quick look and found two things that I think could lead to trouble - one on my end and one on your end. The one on my end should be easy to fix. I have tried to do so, so please try to redownload the new version of the program and rerun the analysis. The one on your end is that I think your example file contains frequency info for 100 sites but your beagle file only contains data for 99 sites (it has 100 lines but the first one is a header). After fixing both issues the program runs without any issues on your example data on my computer. I hope it does on yours as well?

All the best,
Ida

[idamoltke]

ps. Right now the program assumes that your marker names consists of a chr name/number and underscore and the position. So e.g. chr1_10384. If this is not the format you are using then that might get you into trouble as well.

[tristanpwdennis]

Hi Ida
I hope you and your little one have recovered ok, thanks for getting back to me. I pulled the updated version and fixed my freq file and that's working ok now :)
Thanks for all your help!
Tristan