I have one problem at the very beginning of the exome sequencing analysis, probably something wrong with the data format. In general, I have a patient with an unknown mutation and I want to compare the data with the parents to get some candidate genes. So far so good. For Whole Exome Sequencing a company was instructed and they have sent us the BAM files. I have tried to follow the described plan for exome sequencing. Therefore, I want to use the Free Bayes but it did not work, even with the others. Every time the following error indication appeared: Sequences are not currently available for the specified build. Afterwards, I tried to go one step back and convert the bam files into sam files. Fortunately, this worked. But it is not possible to convert this sam files again into bam files. Again the error indication appears as before. Has someone an idea what’s wrong with this bam files and how I can solve this problem? I had to upload the files with ftp because of the size, could this be a problem? I am very unexperienced in this field and deeply grateful for every hint.
Thanks a lot and best regards, Nadja