Greetings,
I am aligning pooled sequencing data to a new renferece genome. GATK won't generate intervals because not every scaffold in the reference is found in my bam index?
What am I missing? It seems like what I am trying to do isn't unreasonable.
INFO 15:52:42,596 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.5-3-gbb2c10b):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation <http://www.broadinstitute.org/gsa/wiki>
##### ERROR Visit our forum to view answers to commonly asked questions <http://getsatisfaction.com/gsa>
##### ERROR
##### ERROR MESSAGE: Couldn't read file /home/zkronenb/Projects/xxx/reference_assembly/withoutsanger.fa because Sequence dictionary and index contain different numbers of contigs