Liftover Gvf From Hg18 To Hg19

Question

[hershman]

Hi,

I'd like to liftover a few gvf files form hg18 to hg19. Do tools exist for this purpose? While the gvf format is supposed to be an extension of gff3, I couldn't get liftover or the gff3ToGenePred tools to accept the files.

Thanks!

[gupta.ne]

hey..even i am trying to liftover GVF files from hg19 to hg18...Did u get any solution for that.Is there a GFF to GVF converter otherwise...I tried searching but could not find any as such.Thanks

Answer 1

[Zev.Kronenberg]

Edit: What kind of errors are you getting?

Edit2: I wrote two perl scripts to make this process go easier. They are not polished code. See below

https://github.com/jewmanchue/zk_tools

grGVF2GFF3 convert your gvf -> gff3

use the UCSC lift over tool

convert back to gvf with LIFTOVERGFF2GVF

I have done this using liftOver from UCSC. Here is the link to the tool:ucsc downloads

GVF should lift over as a GFF3/GFF. If you have any problems let me know.

[hershman]

I tried using the liftover tool, but it gave me a warning: WARNING: -gff is not recommended. Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'

ldHgGene is no longer supported and the new version of the tool (gff3ToGenePred) gives an error: Input file must conform to the GFF3 specification:

The input file that I'm using came from dgv (ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd59Durbinetal2010/gvf/)

[Zev.Kronenberg]

I ignored those warnings. You can spot check that the reference base for any given coordinate matches hg19 on the UCSC genome browser. Everything looked fine in the output.

[hershman]

I would but the mapped file ended up being just a header and the unmapped file had all of the lines

Answer 2

[deanna.church]

The NCBI liftover tool natively takes multiple file formats- including gvf and vcf. http://www.ncbi.nlm.nih.gov/genome/tools/remap