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Picard 2.10.2 is now available at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

# Mouse VQSR

Member

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!

Tagged:

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?

• Member

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.