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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

Converting Reference Genomes from b37 to hg19

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    woodword

    Maybe this will help you:

    https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies#comparison

    In addition you should read this:

    For these builds, the primary assembly coordinates are identical for the original release but patch updates were different. In addition, the naming conventions of the references differ, e.g. the use of chr1(in hg19) versus 1 (in b37) to indicate chromosome 1, and chrM vs. MT for the mitochondrial genome. Included decoys were also different. So it is possible to lift-over resources from one to the other, but it should be done using Picard LiftoverVcf with the appropriate chain files. Trying to convert between them just by renaming contigs is a bad idea. And in the case of BAMs, well, the bad news is that if you have a BAM aligned to one reference build but you need the other, you'll have to re-map the data from scratch.

    (https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19)

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    Genevieve Brandt (she/her)

    Thank you for your contribution woodword!

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    Brian Wiley

    Apparently there is no hg19 to b37/HumanG1Kv37 chain file?  Only the other way around b37tohg19.

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    Genevieve Brandt (she/her)

    Hi Brian,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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