Liftover Of Na12878 Coordinates Into Hg19 Coordinates

Question

[Geparada]

Hi!!

I generated a NA12878 alternate genome file NA12878/hg18 VCF file and the hg18 assembly available on 1000 Genomes ftp server using GATK tools. Now I'll map RNA-seq reads to this genome and generate a BED12 file with the regions of my interest.

In order to compare this results with my previous work, I need to transform the BED12 coordinates, based on the NA12378 genome, into hg19 coordinates.

Can you suggest me a good way to this?

Thanks for your time!!

[Malachi Griffith]

Detailed post on tools for converting genome coordinates between builds: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

Answer 1

[Pierre Lindenbaum]

use the liftOver binaries: http://hgdownload.cse.ucsc.edu/admin/exe/ and the associated files: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/