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sample re-align and recalibration
Dear GATK team
I have around 20 exome-seq samples, and every 2 samples are barcoded and sequenced in one lane. After having generated the bam files for each sample individually with BWA, I was just wondering which is a better way for GATK realignment and recalibration.. shall I just make the alignment and recalibration for individual exome-seq samples, or shall I just merge samples from each lane and process them at the lane level, or should I just merge all the samples and process everything together?
Thank you for your kind advice!