gl.download_ref(), not clear how to use it

[Delvalle-beep]

Hello! All is well? Could you explain me better how to use the reference file to annotate genes "GENENAME", please? Is it the same method for regional plot and manhattan? From the documentation I didn't think it was very clear, I tried to download the file and put anno='GENENAME', but it didn't work

[Cloufield]

Hi, if it is just for annotating "GENENAME", gwaslab will automatically download references (gtf) and process the files when you run it for the first time.

For regional plots, you usually need a vcf file for LD calculation. You can check the available refernces like:

Then use "gl.download_ref()" to download the vcf you need like gl.download_ref("1kg_eas_hg19"):

Finnally, create the regional plot: Regional plots and manhattan plots use the same files for annotate GENENAME. The path for downloaded file can be obtained using gl.get_path("1kg_eas_hg19")

mysumstats.plot_mqq(skip=2,
                    mode="r",
                    region=(7,126253550,128253550),
                    anno="GENENAME",
                    vcf_path=gl.get_path("1kg_eas_hg19"))

Please let me know if you have more questions.

[Delvalle-beep]

When I put "GENENAME" the name of the gene simply does not appear

[Delvalle-beep]

[Cloufield]

Hi, It seems that there were no errors. Could you please show the command you used and also the log? These will help me pinpoint the issue here...

[Delvalle-beep]

Just to finish the problem, I managed to solve it! I'm trying to automate plot generation for my study using your script (: And for some reason I couldn't assign the name of the gene due to the script automatically treating this variable as a boolean