Import CNV.VCF file using Hail

Hail Query & hailctl
1

Hi Hail community,
I have tried to import CNV.VCF file using import_vcf function, but I got empty result when I tried to show the data. What happened? Is there any way to import cnv.vcf file using import_vcf ?

  vds=hl.import_vcf('/home/quang/Downloads/gvcf/300-1.cnv.vcf.bgz',reference_genome='GRCh38')
  vds.head(20)
2

Hey @biodev

You need to use .show() to show the data. .head just truncates the Matrix Table.

You might also find Filtering is really fast but show is really slow, why is that? - #2 by danking and Counting rows in hail table - #2 by danking helpful in understanding how Hail works.

3

@danking Yes. Thanks alot :grin: