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

Error running mutect2 on SAM files remapped to hg38 (original reads were aligned to hg19).


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    Genevieve Brandt (she/her)

    Hello zdr j,

    For your CrossMap error, it looks like the sequence dictionary is malformed for some reason. You can recreate it using a gatk tool: CreateSequenceDictionary (Picard).

    It looks like you are getting a very similar error message from your Galaxy output. Try out the above solution and let me know if it helps.



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