I am trying to follow a tutorial from the GATK team that shows several images with alignments in IGV. The first IGV image in that tutorial shows alignments at a primary or alt locus in chr19. If I understood correctly, these alignments have been mapped with or without considering the alt contigs in the reference genome, so in total there are four different mapping visualizations . Looking at IGV documentation, it looks like that image is a collection of four different screenshots, each showing in IGV the corresponding genome reference and alignments for the chosen mapping mode, but perhaps I missed something, and IGV has actually the functionality to display simultaneously those four visualizations?
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped reads on each genome in a synteny-type view. https://jbrowse.org/jb2/gallery/ https://jbrowse.org/jb2/ this type of workflow I think is actually very useful, and it would be great to streamline it (e.g. looking at reads aligned to different strains in pangenome, etc.) feel free to let me know if I can assist
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and use GenoMax 's suggestion. Thanks again!
You can open multiple instances of IGV and display multiple genome alignments.