Hello list, I already analysed some of our data with your framework and I want to thank you for your great work. But lately I stumbled on some strange behavior - I used the "aaChanges"-tool, as well as the Gene "BED-to-Codon"-tool with the same Gene-BED-File and compared the results. What I did: #example BED-file: chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981 0 16 1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51, 0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553,24049 ,24997,30362, #example-output of "aaChanges" chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T #example-output of "BED-to-Codon" chr17 3773172 3773175 uc002fwt.2 0 - chr17 3773175 3773178 uc002fwt.2 0 - chr17 3773178 3773181 uc002fwt.2 0 - chr17 3775849 3775852 uc002fwt.2 0 - chr17 3775852 3775855 uc002fwt.2 0 - Comparing both results, the "BED-to-Codon" actually presents no codon at position 3775848 - here the fist codon is starting at 3775849. But in fact, looking at the ucsc browser, "aaChanges" is right. There are another few examples (~5/1500 snps) and apparently most of them are positions among the first codon in an exon. Did anyone meet this problem before? What is my mistake? Thank you. Regards Chris