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

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    Arye Harel

    Regarding the first Usage examples on top on of this page:

    What does -L 20 mean?

    If used, it gives the following Error:

    "A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "20" is not valid for this input."

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    GenomicsDBImport seem to freeze when used with reference genome with numerous or larger scaffolds/pseudo chromosomes.

    I got an user error related to the number of intervals which was above 100.

    I have reduced the chromosomes number of the reference fasta file to 15, with a scaffold size between 15Mb and 30Mb, for a total length of 310 Mb.

    But even though the error message don't show up anymore, the script seems to be frozen.

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    JooYoung Park

    Can GenomicsDBImport be resumed if it halts in the middle of the processing?


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