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.
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 \
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.