DepthOfCoverage Error

bgusr

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.

Geraldine_VdAuwera

Hi there,

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

bgusr

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