Entering edit mode
4.3 years ago
vctrm67
▴
50
Posting here because the GATK forums are slow to respond.
To my understanding, BaseRecalibrator requires certain fields, of which includes the platform information. I received bam files in which I do not see any information regarding the platform. Is there a way to add this in? I looked at AddorReplaceReadGroups by the GATK but that only seems to merge everything into a single read group.
Can you post the header of a read. Often one can derive the Illumina platform from the read name.