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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Errors about contigs in BAM or VCF files not being properly ordered or sorted Follow

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    Joel Wallenius

    Hello GATK,

    I realised I was having this issue with the CNV caller tools... but only after the most expensive step that took 10 days on a 256-threaded machine. I don't much want to repeat that if not absolutely necessary. So my question is: Can I somehow edit the order after the fact? The edit would presumably be done on the input files to PostProcessGermlineCalls... I have HDFviewer but am not sure how to make edits with it.

    PS. When I say I have this issue, I'm referring to these lines:

    15:15:19.850 INFO  ProgressMeter - Starting traversal 
    15:15:19.851 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
    15:15:19.853 INFO  ProgressMeter -             unmapped              0.0                     0              NaN
    15:15:19.853 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.

    However, the output VCF file itself looks just fine - the chromosome order may be wack, but there are calls and things in it, as expected. So perhaps the problem is just that ProgressMeter fails when the chromosome order doesn't match the reference fasta (dict) file?

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