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

MarkDuplicates (Picard) Follow


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    What should be the "--ASSUME_SORTED" option if the bam file is sorted by query name?

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    Damian Loska

    are you sure you've set default COMPRESSION_LEVEL to 5?

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