Q:
I noticed that you have an updated version of the GM12878 diploid genome
on the AlleleSeq webpage, but not an updated version of the transcriptome.
Would you be willing to upload an update for the transcriptome as well?
Also, are there major differences between the versions?

I actually now see how to generate the transcriptome myself using
vcf2diploid and the vcf file mentioned in the README (which I hadn’t noticed
before). Do you believe this vcf
(ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.2/hg19/CEUTrio.HiSeq.WGS.b37.bestPractices.phased.hg19.vcf.gz)
is the most accurate?

I’m actually trying to use liftover with the chain files from the newest diploid genotypes you created to update an annotation. However, the annotation ends up being empty. Have you experienced a similar problem? I’m using the hg19 UCSC annotation. Any help you can provide would be MUCH appreciated!

A:
Your chain file does not include ‘chr’ in front of the reference names.