Question: Liftover Of Na12878 Coordinates Into Hg19 Coordinates
gravatar for Geparada
7.1 years ago by
Geparada1.4k wrote:


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!!

vcf bed liftover • 2.2k views
ADD COMMENTlink written 7.1 years ago by Geparada1.4k

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)

ADD REPLYlink written 17 months ago by Malachi Griffith17k
gravatar for Pierre Lindenbaum
7.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

use the liftOver binaries: and the associated files:

ADD COMMENTlink written 7.1 years ago by Pierre Lindenbaum117k
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