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

mergeBam picard issue

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    danilovkiri

    Hi Lucas Kopecky Bobadilla

    The fact that the uBAM is readname-sorted and the mapped BAM is coordinate-sorted is the exact problem causing the error you are reporting. Both uBAM and mapped BAM must be readname-sorted (since uBAM cannot be coordinate-sorted). Try to sort the mapped BAM by a read name.

    "Everything worked fine previously" does not actually mean the data was the same at that time. Unless you can check the sorting order of the BAM files from your previous pipeline runs you cannot presume the error is elsewhere but in the sorting order.

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