Hello,
I am trying to calculate the allele frequency of each variant in a VCF file
I am struggling to figure out the methods to implement.
Any help will be appreciated
hl.variant_qc should do what you need!
Thank you very much
But then I want to write the locus, alleles, location and allele frequency into a text file.
Thats the tricky part
That won’t be tricky. It should look roughly like:
mt = hl.import_vcf(.....)
mt = hl.variant_qc(mt)
rows = mt.rows()
to_be_exported= rows.select(.....<whatever fields you want> .....)
to_be_exported.export("filename.tsv")
Alright. Thank you very much. You have been very helpful