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!!