It looks like it is not able to align the MAF to hg19. I am not sure why this happens. I looked into my MAF and it was built on b37 however I have only 1-22 chromosomes and the format and everything seems to be correct. Any ideas on why this might be happening? Thanks.
Not sure what exactly happened, MutPanning worked pretty smoothly for me and it comes with its own graphical interface which I found pretty intuitive to use. Since the error happens pretty early, I don't think this error has anything to do with Hg19 - I guess its much more likely that the software can't find some piece of information that it needs to execute this job. Did you check the column headers of your maf file? Do they exactly match the column headers that the software expects? Perhaps it's just a minor difference in your maf, such as capitalization, hypen or underscore. Although maf is a standard format different packages produce slightly different versions of maf files and the column headers are spelled slightly differently. The tool comes with a graphical interface that explains all columns and their headers which are required. Also there are exemplary files you can download through the graphical interface - so if in doubt, I would just c+p column header from there. If the column headers don't match exactly, the software won't find all the information that it needs to execute this job. And this might cause your error. If after this check of your maf file the error persists, I would check the sample annotation file. Are the column headers correct? Did you specify all samples from the maf file in that sample annotation file (check for typos)? If the error persists after these checks, you can also try the online version on genepattern to make sure its not a platform issue, but I would first try the other two things since that's far more likely to cause this error... I hope this helps a little, good luck...
