Liftover GRCh37 to hg38 1kg/GATK.

Question

[ManuelDB]

I need to liftover a few variants from GRCh37 to hg38 1kg/GATK. UCSC lifover does not have this reference genome version available. I have tried with the standard hg38 but conversations are wrong. Where can I find GRCh37 to hg38 1kg/GATK chain files or an online tool that do this??

Answer 1

[Giulio Genovese]

You can use the UCSC liftover chain file:

wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz

Or the Ensembl chain file:

wget http://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh37_to_GRCh38.chain.gz

Alternatively you can also use the GATK version of the UCSC chain file:

wget https://raw.githubusercontent.com/broadinstitute/gatk/master/scripts/funcotator/data_sources/gnomAD/b37ToHg38.over.chain

Notice that the UCSC chain file is proprietary and restricted for commercial use while the Ensembl chain file is free for any use. The Ensembl and the GATK version are specifically made for GRCh37 rather than for hg19 and they will work with a tool like Picard LiftoverVcf. However, I would recommend to use BCFtools/liftover if you are working with a VCF. The latter is available here and binaries are available here and since it is flexible with contig names in the chain file you will be able to use any of the three chain files above when lifting over a VCF

[ManuelDB]

Such a good answer! Thank you so much