Chain file for Homo_sapiens_assembly38.fasta to liftover Nebula vcf
Which chain file is needed to convert from positions in a vcf aligned to Homo_sapiens_assembly38.fasta to a vcf with positions aligned to hg19.fa. The obvious solution hg38ToHg19.over.chain.gz did not work. I couldn't find any information in the MEGABOLT bioinformatician guide from MEGABOLT regarding such a chain.file.
Best regards,
Berndmann
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This doesn't work. liftOver and the corresponding chain files can lift over genomic coordinates, but you cannot lift over whole genome assemblies in a Fasta format.
Thanks for the clarification. I have edited my post.