Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GATK 3.5: CRAM file error with samtools-1.3


I recently created a cram file using PrintReads and tried to view the file with samtools-1.3. The header could be viewed just fine, but after the header ended the file was considered to be truncated. I received the following error:

Failed to populate reference for id 0
Unable to fetch reference #0 10001..893888
Failure to decode slice
[main_samview] truncated file.

The cram file size seems appropriate and could even be converted back to a BAM file with PrintReads successfully. I am not sure if this is a compatibility issue and if so is there a fix in the works.

Vito C.


Best Answer


  • vcaropre1vcaropre1 Member

    Yeah this version of samtools supports cram. They use a .crai index file and I created one with samtools and still the same error was reported. I will contact them about the error as well.

    I created a cram file through samtools-1.3 and could view it and GATK 3.5 could recognize the file and process it without an issue.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ok, let us know what the samtools folks say. We're all just starting to support cram so I wouldn't be surprised if we had some incompatibilities. Sorry for the inconvenience.

  • vcaropre1vcaropre1 Member

    Just heard back from samtools. Simple fix. For samtools to open the cram file created by GATK it must have the reference sequence added with the -T flag. So it would look like:

    samtools view -h cram_file -T reference_file_used_to_make_cram_file

    This overrides the attempt to pull the reference via HTTP and uses the file instead.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, that makes sense, good to know. Thanks for reporting back with the solution!

Sign In or Register to comment.