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Questions about the GATK hg38 resource bundle reference

jejacobs23jejacobs23 Portland, ORMember

I am using the GATK hg38 resource bundle reference in my workflow and I was curious if there is any documentation or literature on how the contigs were chosen. Specifically, were did all the decoy contigs come from? A second part to my question is how decoy contigs are managed in a variant calling workflow. Are they ignored by Mutect2 or do you have to filter them out?

Answers

  • AdelaideRAdelaideR Member admin

    Hi @jejacobs23

    A detailed description of what is in the resource bundle can be found here

    These resources are provided as a starting point, but it is up to each individual researcher to determine if these are the best resources for their analysis.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited May 17

    @jejacobs23

    As far as decoy contigs, you can use MateOnSameContigOrNoMappedMateReadFilter to filter out alternate contigs should you choose to do so. Mutect2 disables this filter by default.

  • jejacobs23jejacobs23 Portland, ORMember

    Thank you @AdelaideR for your response

    I was more curious as to how the decoy contigs were chosen. There are quite a lot of them in the GATK hg38 build as compared to other versions of hg38 that I've looked at. I didn't know if there was a specific criteria that was used to include decoy contigs.

  • jejacobs23jejacobs23 Portland, ORMember

    Thank you @SChaluvadi

    I'm concerned that if I use the MateOnSameContigOrNoMappedMateReadFilter, I will loose variants that are mapped to alternate contigs. After giving it some thought, I was considering using my interval list to exclude decoy contigs while retaining the other alternate contigs. Do you think that is an appropriate way of dealing with the issue?

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