I am currently working on a WGS project and I would like to ask whether there are specific restrictions on the choice of the short read aligner. Can a particular aligner be used for both RNAseq and WGS work? Or are there peculiarities that limit the application to either RNAseq and WGS?
Specifically, can BWA be used in RNAseq? Or can HISAT2 or Bowtie2 be used for WGS? What would be the impact on the downstream application, for instance, the structural variance assessment? Would fo instance the SAM files produced by HISAT2 be recognized by on Picard or GATK the same way as are those produced by BWA? would HISAT2 provide the 'read group' heading, for instance?