Does anyone know how to merge two BWA alignments into one using samtools? I have a pe read alignment and a contig alignment, both done with BWA and I was wondering how difficult it would be to merge these into one consensus alignment?
The authors of the following paper (Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution)
did this with contigs and mate-pair reads:
"The BAM format alignment files of the contig mapping and the mate-pair read mapping were subsequently merged using SAMtools suite v0.1.18 "