Given a single DNA sample extracted from swab and these two cases:
Prepared a single library and sequenced it 3 times separately
Prepared 3 different libraries from the same DNA sample and sequenced each library
Both cases result in 3 sets of fastqs. Case 1 representing technical replicates for sequencing. Case 2 representing technical replicates for library prep.
If the goal is perform variant calling. How should I treat the fastqs from these two cases? Should I merge fastqs and then map/variant call? Should I keep them separate and somehow merge the gvcfs/vcfs? Are there variant calling methods/software that can take advantage of batch information?
How important is sequencing/biological batch information in terms of variant calling?