If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
How to judge convergence on BQSR
A nice day to you! Someone said "When the plots of BQSR don't change dramatically, it is convergence." I generated a pdf file afer the command
java -Djava.io.tmpdir=/mnt/tmp -jar $GATKPATH/GenomeAnalysisTK.jar -T BaseRecalibrator -R $REF -BQSR first_round_recal_data.table -before second_round_recal_data.table -after third_round_recal_data.table -o output.pdf
And I got the output file. Could you tell if my dataset convergence? Which part do I need to focus on during judge (which parts should be compared)? Thanks for your generous helping