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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

BQSR for RNA-seq data

I am working on calling variants in my RNA-seq data using the GATK best practices pipeline. I have made it through step 3 (split and trim and reassign mapping qualities). I then got to indel realignment which was labelled as optional and I skipped this step. Now I am at Base Recalibration and I am having trouble understanding the tool documentation. The documentation says to run the following script:

java -jar GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-R reference.fasta \
-I my_reads.bam \
-knownSites latest_dbsnp.vcf \
-o recal_data.table

My question is, how am I supposed to make the "KnownSites latest_dbsnp.vcf" file? Also, when I have finished this step, how do I use this info to get a recalibrated bam file for the variant calling in the next step? Thank you very much for your help.

Best Answer


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