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

MergeBamAlignment (Picard) Follow

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    Jared Grummer

    Hello, I'm trying to follow the best-practices for generating "clean" bam files (from here:, but I get an error when using the output of the MergeBamAlignment step in the next step, MarkDuplicatesSpark. I get this error “Detected multiple mark duplicate records objects corresponding to read with name XXXX, this could be the result of the file sort order being incorrect or that a previous tool has let renames span multiple partitions”, and I can see that that read is indeed listed twice (4 entries, paired-end reads) in the bam output of the MergeBamAlignment step, even though I have set the 'INCLUDE_SECONDARY_ALIGNMENTS' flag to false. Do you know what the problem is? I have tried searching and trying different options in bwa mem and MergeBamAlignment, but can't make this problem go away! Thanks in advance!

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