I have been using satsuma synteny to assign scaffolds (from the genome of my study species) to the chromosomes of a closely related species. I now have a tab delimited file that lists these scaffolds in the order that they need to be placed and wondered if there was a way I can use this to reorder (and orientate) a vcf file?
The tab delimited file has the following columns: Chromosome number (of closely related species), Scaffold (of my study species), Mean location of scaffold, Scaffold orientation.
I also have a separate file containing scaffold lengths (just in case that info is also needed).
Does anyone know how I could do this? I am relatively new to bioinformatics and have been struggling to figure this out for a long time!
Thanks Ash :)