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

ReadsPipelineSpark (BETA) Follow

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    I am finding that MarkDuplicates and this tool ReadsPipelineSpark mark a different number of reads as duplicate (flag > 1024). Same version of gatk ( Why is this the case? any configuration we need to make sure that they are the same? 

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