Hi all, I used samtools index to index cram files and tried to view the data in the Integrated Genomic Viewer (https://software.broadinstitute.org/software/igv/). The samples are whole-genome sequencing data from S. cerevisiae.
We have downloaded the cram files from our collaborator and I have simply used the default samtools index command to index the cram file. I did not get any errors at this stage. For some files I'm having problems viewing certain parts of the genome. However, for other files (from the same batch and using the same ref genome and alignment method), I can view the exact same region just fine. The error in IGV is as follows: Error - possible sequence mismatch (wrong reference for this file): htsjdk.samtools.cram.CRAMException: Reference sequence MD5 mismatch for slice: sequence id 10, start 1, span 666454, expected MD5 c831338ca9079d76bebd0b0a5eb102ef I have attached one cram index file that gives this error when looking at e.g. YKR002W on Chr XI. I haven't attached the corresponding cram file because it is rather large (200 MB), but if needed I can try to send this or other info that is missing. Since I'm new to the cram format, and samtools in general, I'm not sure whether the issue arises during the indexing with samtool and how I could check this. I would be very happy with any troubleshooting tips! I'm using: samtools 1.14 Using htslib 1.14. Thanks, Sabine
42363_4#33.cram.crai
Description: Binary data
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