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?