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

Mutect w/ panel of normal throwing errors, even though mutect w/o panel of normal works fine.


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    Gökalp Çelik

    Hi Eduardo Maury

    Based on the error message you posted It looks like some of your input files are in sam format rather than bam format. You may be able to check their bgzip compression status by just typing

    cat filename | head -n 10

    If you get a meaningful text header then the file is not bam but sam format. You may be able to convert them to bam using gatk PrintReads or samtools view. 

    I hope this helps. 

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