Use Table with Variants to filter MatrixTable from VCF File

Hail Query & hailctl
1

Hello,

I am trying to filter/join MatrixTable from VCF file and Table with Variants on alleles and locus.
Can you help me with the code? What is the right way to do it?

Best,

1 Like
2

some code:

mt1 = hl.methods.import_vcf(vcf_file, contig_recoding=recode, force_bgz=True)
var = pd.DataFrame({'chrom': ['1', '1'],
                  'pos': [12783, 13116],
                  'ref': ['G', 'T'],
                  'alt': ['A', 'G']})
ht = hl.Table.from_pandas(var)
ht1 = ht.key_by(**hl.parse_variant(ht.chrom + hl.literal(':') + hl.str(ht.pos) + hl.literal(':') + ht.ref + hl.literal(':') + ht.alt))

and now I want to get from mt1 only the rows with locus and alleles which are in ht1

3

ht = hl.Table.from_pandas(var)
ht = ht.key_by(**hl.parse_variant(ht.chrom + hl.literal(‘:’) + hl.str(ht.pos) + hl.literal(‘:’) + ht.ref + hl.literal(‘:’) + ht.alt))
ht = hl.MatrixTable.from_rows_table(ht)
ht = ht.select_rows()
ht = ht.select_cols()
ds_result = mt1.filter_rows(~hl.is_missing(ht.index_rows(mt1[‘locus’], mt1[‘alleles’])))
ds_result.show()

this is the code