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BaseRecalibration or IndelRealignment first?
I asked this question in a comment under BestPractices but never got a response. Hopefully I will here. Here goes:
I have been running GATK v1.6.2 on several samples. It seems the way I had initially had run GATK for indel-realignment and quality re-calibration steps are reversed. For example, in order of processing, I ran:
- Count Covariates
- Table Recalibration
- Realigner Target Creator
- Indel Realigner
What are the consequences and effect to SNP and INDEL calling if the GATK steps are ran as above?. I'm aware that this is not according to the best-practices document (thank you for the thorough GATK documentation), but I wanted to know if it is essential for me to re-analyze the samples. The variant caller I'm using looks at BaseQuality scores when making calls.
Any help on this would be appreciated.