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

CollectHsMetrics (Picard) Follow

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    One question I've seen repeatedly on several sites is about the difference between what exactly the bait and target intervals are supposed to represent.  It would be extremely useful if that explanation was included here (i.e. that the  --TARGET_INTERVALS are typically just the exons, while the --BAIT_INTERVALS are typically wider regions)  in the explanation of the command line options rather than having to figure it out by deciphering it from the Picard Metrics definitions.  

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