Hi all,
I saw that several people have had similar issues with this tool but none of the solutions really clarified what the issue is here. I have BED files with genomic regions that I got using the GRCh38 reference sequence. Because Galaxy only has up to hg19 built in to the Extract Pairwise MAF Blocks tool, I uploaded aligned MAF files to my galaxy history from the UCSC Downloads area to my local computer and then unzipped before uploading to my Galaxy History (the path to the reference: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsRheMac8/hg38.rheMac8.synNet.maf.gz).
However, when I open the tool and select my BED file with my genomic intervals, I get an error message pop up that there are no options available for my MAF source. The MAF file is imported in as an MAF and has been labeled as being aligned to GRCh38, so there shouldn’t be any incompatibilities between my MAF and my BED. Does anyone know what’s going on?