thanks for developing the tool! I have been running it successfully over the last couple of weeks. I have a few questions that would help in polishing and generating the final results:
The ABF prior of 0.04 is based on a previous work by Wakefield. Do you know what are the risks of using a higher value? I've seen a linear increase in PIPs when changing the default value of 0.04.
As seen in the above example, in the first panel some dots appear in gray color. I have seen this to varying degrees, and in some other analysis most points are in gray. Would this mean that they are not in gnomAD only?
Is it possible to use a different annotation for the plotting scripts? I've noticed that the one used for the locus zoom plots (as shown above) has some differences with the one available at NCBI, and would like to generate the plots with the NCBI one.
Thanks for your time, and looking forward to your responses!
Hi!
thanks for developing the tool! I have been running it successfully over the last couple of weeks. I have a few questions that would help in polishing and generating the final results:
As seen in the above example, in the first panel some dots appear in gray color. I have seen this to varying degrees, and in some other analysis most points are in gray. Would this mean that they are not in gnomAD only?
Is it possible to use a different annotation for the plotting scripts? I've noticed that the one used for the locus zoom plots (as shown above) has some differences with the one available at NCBI, and would like to generate the plots with the NCBI one.
Thanks for your time, and looking forward to your responses!