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:

    gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.with_assay_info.haplotype_database.txt

    gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.with_assay_info.haplotype_database.txt

     

    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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