dbSNP version for GATK best practices pipeline
The GATK data resources bundle for gatk best practices contains dbsnp ver 138.
Is it possible to use an updated version (like v151) for bqsr & vqsr ? or it is recommended to use the same version as in the bundle (138) ?
Thanks
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Hi,
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Hi Chadi Saad,
Yes, you can build your own resources and run these commands with the newer versions of dbSNP. It looks like one user ran into an issue last year, but a fix has been implemented: https://gatk.broadinstitute.org/hc/en-us/community/posts/360062537671-GATK-4-1-7-0-does-not-annotate-ID-using-dbSNP-build-153-VCF
Best,
Genevieve
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Thanks for your reply.
Actually my comment was about tools like Indel-realigner, VarQual recalibrator. Not about annotation.
Is it possible to run this tools using a new version of dbSNP (after splitting the multiallelic variants as you suggest) ? or for quality matters, it's better to use the bundle version (138) ?
Thanks again
Best
Chadi
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Yes, I saw your comment was regarding those tools, but potentially the other example could be helpful as well.
There shouldn't be issues from changing the dbSNP version, but it is best to be consistent with your pipeline and analysis.
Here is a question from our old forum with someone using a different dbSNP version, for more information as well: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2017-06-18-2017-01-18/9382-How-to-get-rid-of-false-positives-And-troubles-with-VQSR
Genevieve
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