Sort vcf file based on Satsuma synteny output

Question

[ash.t.cook]

Hi all

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 :)

Answer 1

[clinnaeus]

Hi ash -

Did you ever figure out how to do this? There is shockingly little information online about trying to do exactly this, despite it being a presumably common step!