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Hello, I was wondering if there's any particular reasons why gene_bed path is missing in conf/igenomes.config. I haven't checked all the genomes but for GRCh37, the BED file generated by makeGeneBED has the same number of lines as the one located in s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed despite the difference in the order of a few rows. So I tend to believe they are identical. I understand you still need to have a process to generate BED files for those uncommon genomes. But it may save users some time and computing resources when it comes to human or mouse samples.
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