Could not able to export the data to ElasticSearch


You’ll need to create an entirely new reference genome – not add sequence to GRCh37 (this is used to add a fasta file for reference base lookups).

This will look something like

hs37d5 = hl.ReferenceGenome(name='hs37d5', contigs=['1', '2', '3', ...], ...)

Then you’ll need to use this reference on import.


Thanks @tpoterba, it helps. Great work.


Hi @tpoterba,

Is there a way, I can add hs37d5 to the existing contigs of GRCh37?



You can build a new reference genome based on GRCh37, but you cannot modify the existing GRCh37 - this is a somewhat nonsensical thing to do, since GRCh37 is a well-defined reference genome and does not contain a hs37d5 contig.