Genome Analysis Toolkit

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

Sequence dictionary and index contain different numbers of contigs

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    Genevieve Brandt (she/her)

    Hi rahelp, there could have been an issue when you downloaded the files and created the index and dictionary files. Check for errors in those processes and/or re-do them to confirm the files do not have issues.

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    Genevieve Brandt (she/her)

    rahelp another user is seeing this same error message. Did you end up solving this problem? If so, what was your solution?

    Thank you,

    Genevieve

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    rahelp

    Dear Genevieve,

    The issue was that CreateSequenceDictionary was not working properly.

    For it to work properly:

    • google authentication completed
    • Docker default memory is only 2 GB. This needs to be set to higher (I set it to 100).
    • change java options: 

      gatk --java-options -Xmx12g CreateSequenceDictionary -R Homo_sapiens_assembly19.fasta

    I hope this helps.

    Good luck!

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    Genevieve Brandt (she/her)

    Thank you so much, rahelp!

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