Performing liftOver between genome assemblies not available on UCSC genome browser

Question

[br.tania]

Hi All,

I have VCF files for 2 different macaque species' (Pig-tailed, Japanese) samples. The aim is to liftOver the VCF from one specie to the other. This can be done with the UCSC Genome Browser except their genome assemblies are not available on the Browser yet. So I need to find a way around it.

I came across this pipeline to make the liftOver files [http://genomewiki.ucsc.edu/index.php/LiftOver_Howto]. If I do this, how will I then liftOver between the VCF files?

Further, is there any tool out there which can use 'new' genome assemblies to liftOver coordinates from one VCF to another? For instance, I saw CrossMap [http://crossmap.sourceforge.net]. It requires UCSC chain files as input. Following the pipeline link I mentioned above, I could make a chain file (make it, then sort it), not go till the liftOver file - that could be used as input to CrossMap then?

I am on a deadline so I want to be sure before beginning the process that CrossMap would work if I make the chain files by myself for genome assemblies not available on UCSC Genome Browser yet.

I appreciate any inputs and comments on this.

Thanks in advance.

Answer 1

[colindaven]

It might be quicker and more accurate to realign and recall the SNPs. Especially if you are looking at more complex analyses later like gene presence absence or SVs.

I always had issues trying to work with chain files and so on from UCSC. Especially because it was not all free for non-academic users.