Running FUMA with GRCh38 positions

[Jaehyun Park]

My name is Jaehyun Park. I am a postdoctoral research fellow at Vanderbilt University Medical Center.

I would like to send an inquiry about running FUMA with files with the variant positions in GRCh38.

I have a summary file with the positions that correspond to the GRCh38 build.

I put the file and entered the column names for the positions and the alleles, but the button for using GRCh38 was not activated.

I found a previous thread, about a year ago, that the feature was paused because of the issues it caused.

build 38 button

I would like to ask whether there is any update for this issue.

I would appreciate it if you could give me a response.

Thank you.

Best regards,

Jaehyun Park.

[Tanya Phung]

Dear Jaehuyn, 

Thank you for your message. 

At this time, unfortunately GRCh38 feature is not yet available. You can always use UCSC Liftover tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert the positions to GRCh37 before submitting to FUMA. 

FUMA is a free tool but requires a lot of resources (both computational and human) to support, maintain, and add new resources. We are constrained by our availability and priority because we also have our own research projects to work on. Adding support for GRCh38 is on the agenda but there are also other tasks that take priority. Thank you for understanding.

Best,
Tanya

[Nik Tz]

Hi Tanya and team,

Many thanks for the great software. Any updates on GRCh38 support please?

Also is it possible to produce some output to indicate number of variants dropped from the input due to non-annotation against the LD reference panel please?

Thanks, Nik