Converting Genome Reference Consortium to UCSC, i.e. GRCh* -> hg*
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7 weeks ago

I am wondering how to convert a GRCh* file to its corresponding hg*. I would like to do this as part of the process to use a GRCh37 VCF file for analysis w/ an hg38 reference, ideally convert the GRCh37 to hg38 directly, or at least to hg19 (and then to hg38).

Using LiftoverVCF with hg19ToHg38.over.chain.gz doesn't seem to work for me because of scaffold naming differences between the GRCh37 VCF and entries of the chain file, such as the "chr" in GRCh* and not in the chain file.

Would someone be able to suggest an option, or point me to a liftover file that will do the conversion I am looking for? Thank you.

GRCh37 GRCh38 Liftover hg38 hg19 • 123 views

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