I have processed exome seq files following GATK Best Practices.
I was to run joint genotyping with a interval list (format: BED) and faced with an error message like this:
ERROR MESSAGE: Badly formed genome location: Contig 'Interval' does not match
any contig in the GATK sequence dictionary derived from the reference; are you sure
you are using the correct reference fasta file?
It embarrassed me because I did not see error message when I run haplotype Caller with a same interval list and reference file.
I tried to use a revised interval list (0-based to 1-based using simple coding work), but nothing better.
And I have not found similar problem with me in GATK Forum.
Please let me know how I have to do.
Thanks for any comment.
