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

RevertSam (Picard) Follow

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    Eugene Albert

    Hi, I was trying to remove MD and MN tags with the following command: java -jar ~/bin/picard.jar RevertSam --INPUT test.sam --OUTPUT test.reverted.bam --ATTRIBUTE_TO_CLEAR MD --REMOVE_ALIGNMENT_INFORMATION false --REMOVE_DUPLICATE_INFORMATION false --RESTORE_ORIGINAL_QUALITIES false --RESTORE_HARDCLIPS false

    And it does nothing to the input file, leaving the tags untouch. I'm not sure is it my mistake or the bug due to nontarget usage

    Best, Eugene

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