Attention: Want an end-to-end pipelining solution for GATK Best Practices?
I am getting the following error when running DepthOfCoverage:
ERROR MESSAGE: Reference index 85 not found in sequence dictionary.
I have already reheadered my bam file to fix a contig mismatch error, and the fasta dict file was generated automatically by gatk. Moreover, about 160 lines of output are generated, but I do not see any irregularities at the position where the code crashed. Please let me know what I can try. Thank you.