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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

Where do I find GATK v2.8-1?

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    elcortegano

    Ok, I found a tarball here: https://github.com/broadgsa/gatk-protected/releases/tag/2.8

    I guess I want to reformulate my question as how to find the jar file of this version, pre-compiled.

    It is proving much challenging to compile this version from source.

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    Pamela Bretscher

    Hi elcortegano,

    This version of GATK is significantly outdated and no longer supported by the GATK team. The response on the ticket you linked is correct in that these annotations are no longer stored for reference sites but that you should be able to get QUAL scores for reference sites in GenotypeGVCFs -all-sites mode. If you would like to attempt to use the older version, there may be other users who could help you access it, but it is not supported by the GATK team.

    Kind regards,

    Pamela

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    elcortegano

    Hi Pamela, thank you for your feedback,

    The problem with `GenotypeGVCFs -all-sites` is that in gatk v.4.x (and v.3.x) is that I do not get QUAL or MQ for any invariant site (wonder if might be due to the use of `ploidy 1`). This is what was the issue posted in the Github, and at the moment don't know if it has or will have a solution, hence the need of using an older release (also for reproducibility).

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    Pamela Bretscher

    Hi elcortegano,

    The ploidy should not have an impact because GenotypeGVCFs can work with any ploidy. The MQ and QUAL annotations identify the confidence in a variant call and are therefore dependent on a site having alternate alleles. This is why those annotations aren't being calculated for invariant sites. Is there a reason why you need these annotations for invariant sites? I am unable to help you in using the older version of GATK, but other users may be able to provide some insight. 

    Kind regards,

    Pamela

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    elcortegano

    Hi Pamela,

    The need for QUAL and MQ at invariant sites mainly comes from "backward" compatibility with a 2015 Genome Research study (https://pubmed.ncbi.nlm.nih.gov/26260971/). There, de novo mutations were detected as variants in GATK, but in order to compute mutation rates, a "callable" fraction of the genome needs to be defined. In that study, that was done using QUAL and MQ values from invariant sites, with GATK 2.8-1.

    We now want to do a study using the same biological material and want to perform comparisons in terms of callability and mutation rate. For that, we also want to be able to define callability in the same terms as before, using QUAL and MQ at invariant sites. We are ok changing version numbers for GATK, but for fair comparisons it would be desirable to use the same definition of callable genome as before.

    Hope that makes sense,

    Thanks,

    Eugenio

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    Pamela Bretscher

    Hi elcortegano,

    Yes, this makes sense and I understand why you want to be able to recreate the study using the same parameters. I don't think using QUAL and MQ at invariant sites is applicable to GATK 4, so it may not be possible to fully reproduce these values without using the older version. However, given the significant updates to GATK in the years since GATK 2, I would suggest that it would probably be more beneficial to update the definition of "callable", rather than rely on the error-prone and outdated version of GATK.

    Kind regards,

    Pamela

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