I was trying out transformation with the VCF files as shown below
mt2 = mt.select_entries(mt.GT) mt3 = mt2.annotate_rows(n_hom_ref=hl.agg.count_where(mt2.GT.is_hom_ref()), n_het = hl.agg.count_where(mt2.GT.is_het()), n_hom_alt = hl.agg.count_where(mt2.GT.is_hom_var())) mt4 = mt3.select_rows(mt3.rsid,mt3.n_het,mt3.n_hom_alt,mt3.n_hom_ref,Ref=mt3.alleles,Alt=mt3.alleles) # this works fine.
However, if I change the last stmt like below, it throws an error.
q1) This is just a matrix table created out of another matrix table. like how we filter and reorder columns in pandas dataframe. But why does it have to be in the specified order?
q2) Any advice/suggestions on the code that I wrote above for getting the below-expected output? Is there any other better way to write this?