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

BQSR Illegal Argument Exceptions


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    David Roazen

    Hi Alexander Sun,

    This error could be caused by an unusual/problematic CIGAR string in one of your reads. For example, a CIGAR beginning/ending with a deletion. Have you tried running ValidateSamFile on your bam? Unfortunately the error message does not tell us the specific site where the failure occurred. If you're able to share your inputs to BQSR with us, we'd likely be able to track down the source of the error for you.



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