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Mouse VQSR

I was wondering if anyone has used VQSR for a mouse related genome project. I am working with mm10 dbsnp and DNA-seq short insert data for multiple homozygous mouse samples. I have obtained decent results so far using the mm10 dbsnp as the training set, but was curious to see if anyone had any recommendations as to what settings to use. Any input is appreciated. I also have a lot of RNA-seq data, but that will come at a much later point in time. Thanks!

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    We do not have any mouse-specific recommendations, but I know we have other users who work on mouse genomes. Hopefully someone will volunteer to share their experience with you.

    In relation to this, we are considering setting up subcategories in the forum to consolidate organism-specific discussions. Is that something you would want to use to connect with other researchers who also apply GATK tools to the organism you study?

  • Yeah I think that would be very helpful. I have another question though. What are the key differences between SNP mode and INDEL mode when running VQSR? I have run in both with similar settings, and the number of variants filtered are almost identical. I have also run in BOTH mode and a significant amount of variants were left unfiltered compared to the other two modes.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    The main thing you should consider when deciding which mode to use for VQSR is how your variants were called in the first place. If you called them together using the same caller, applying the same statistical model, then it is okay to filter them together too. But if you called them separately then merged the results, you shouldn't filter using BOTH, because some of the metrics will not be comparable directly. When in doubt I would recommend performing the procedure separately.

  • Okay thanks. That makes sense

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