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

Detecting sample swaps with Picard tools Follow


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    Yossi Farjoun

    We finally got approval to make public the full "haplotype database" that we use in production. These are designed for human samples:




    Note that some assay information is included in these files and we are allowed to say that at the Broad we were using the sites listed under "fluidigm_96plex_v1".


    I hope this is useful for someone.



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    Yossi Farjoun

    We finally got the thumbs-up to publish the actual snp list that we use for can find it here.


    Also, in case you were wondering what system we are using for assaying the's the description:

    "The Broad utilizes Fluidigm Corporations BioMark HD dPCR system. This platform is based on microfluidic chip technology, requiring less sample and reagents while still achieving high-quality, consistent results. Custom primers are used throughout the process. A multiplexed pre-amplification step (STA) allows for target enrichment. Samples are diluted post-amplification and added to the Sample Loading Reagent (SLR). Assay plates are prepared and the IFC (Integrated Fluidic Circuit) Chip is primed utilizing the IFC Controller HX. Sample and Assay are both added manually into the wells on either side of the IFC. Samples are loaded into the wells on the right side of the chip; assay reagent
    is loaded into the wells on the left side of the chip. Once all wells are loaded, the chip is again placed into the IFC Controller for loading. Once loading is completed, the chip is placed in the FC1 thermocyclers for amplification, followed by scanning on the Biomark HD. Scoring and analysis is performed utilizing the Genotype Analysis Software from Fluidigm."



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