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DepthOfCoverage Error

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


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,581Administrator, GATK Developer admin

    Hi there,

    It sounds like you broke something when you fiddled with your bam file header. Have you validated your file?

    Geraldine Van der Auwera, PhD

  • bgusrbgusr Posts: 2Member

    Thanks! You were right. The issue turned out to be with the bam file itself.

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