import hail
hail.init()
kova = hail.import_vcf("/Users/hojin/OneDrive/kova/kova_pairwise_test/kova_pairwise_test_hj.vcf", reference_genome='GRCh37')
kova.describe()
kovatb = kova.entries()
kovatb.describe()
kovatb['`AAChange.refGeneWithVer`']
I am using Hail0.2 and I wrote down the following scripts to import the vcf file.
but, I encountered error that some filed names include backtick like AAChange.refGeneWithVer, which makes me can not select filed using field names. And I also tried to use rename(), but it is not work for this case, because in rename({’AAChange.refGeneWithVer’ : ‘AAChange.refGeneWithVer’}), could not recognize AAChange.refGeneWithVer field name.
Row fields:
‘locus’: locus
‘alleles’: array
‘rsid’: str
‘qual’: float64
‘filters’: set
‘info’: struct {
AAChange.refGeneWithVer: array,
AC: array,
AF: array,
ALLELE_END: bool,
AN: int32,
… there are many annotation fields
