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Mixing Paired-End and Single-End Reads
I am calling SNVs from whole genome sequencing data using the workflow outlined in the GATK best practice. My sample has been sequenced both in single and (mostly) paired end lanes. I wish to use all of these data for SNV calling. Other threads suggest that this should not be a problem, but I was just wondering if there are any specific steps for which I should treat these reads separately (i.e. base recalibration).
Thanks in advance,