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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    payal banerjee


    I am trying to follow the mitochondrial variant calling pipeline by GATK I want use RevertSAM. 

    I noticed a couple of options for "ATTRIBUTE_TO_CLEAR" are most probably deprecated. What did they stand for and what the best option to replace them with now, as I don't see FT and CO in list of string options for ATTRIBUTE_TO_CLEAR. The current options are - [NM, UQ, PG, MD, MQ, SA, MC, AS]



    I also noticed RevertSamSpark (BETA). Should I use RevertSam or RevertSamSpark (BETA)? What's the difference?



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