Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

DepthOfCoverage Error

bgusrbgusr Posts: 2Member
edited October 2012 in Ask the team

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.

Post edited by Geraldine_VdAuwera on


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