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

Introducing GATK for Microbes Follow

4 comments

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    xiucz

    hi,

    why not use `Haplotypecaller` to call variants in  microbial genomes?

    Thank you .

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    Shahryar Alavi

    Because HaplotypeCaller assumes that the input genome is diploid, which is not the case with microbial genomes.

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    xiucz

    Shahryar Alavi

    Thank you .

    How about setting `--ploidy ` to `1` for HaplotypeCaller to run on  microbial genomes?

    Best,

    xiucz

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    SdB

    The Github repository hasn't been updated in a few years and the status is marked as 'alpha'. Is this still the recommended pipeline for bacteria SNP+indel calling?

     

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