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.
What is the difference between ApplyRecalibration and ApplyVQSR
I am trying to do quality control for germline SNP & indels in 12 cancer patients. I have completed upto the VariantRecalibrator step. Now I am trying to figure out which tool do I use next ApplyRecalibration or ApplyVQSR. I looked at the documentation of both these functions and they seem to do the same thing. I am looking at this pipeline. Here ApplyVQSR has been used and ApplyRecalibrator function is missing. But in the corresponding documentation ApplyRecalibration has been discussed and ApplyVQSR is missing. I am confused, can somebody explain which one should I be using fpr characterizing germline SNP and indels.
Secondly, I noticed that in the wdl file referenced above, the vcf which is output from the indel mode of ApplyVQSR is being fed into ApplyVQSR snp mode (search for the word " tmp.indel.recalibrated.vcf" in the wdl file). But, I thought snp and indels are evaluated separately. Is this correct?