Hail version: 0.2.21-f16fd64e0d77
Error summary: HailException: Invalid locus ‘5:33661936’ found. Contig ‘5’ is not in the reference genome ‘GRCh38’.
The problem is with the importing the VCF file which is based on GRCh38.
the code is
dbSET=hl.import_vcf(‘38dbsnp.vcf.gz’ ,force_bgz=True,reference_genome = ‘GRCh38’)
dbSET.rows().select().show(5)
Then it is showing error
GRCh38 expects contigs of the form "“chr5”, not “5”.
Use contig_recoding = {'1': 'chr1','2': 'chr2',.......) while importing.
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