Anyone could give me a hand?
can you give an example of what you want? I’m not quite sure based on the title.
I want to extract one specific loci genotype of specific sample
for example, I want to know the “1:10000” loci genotype of sample “NA12878”, I don’t know how to extract from the matrixtable.
thank you very much
This is certainly possible, but it’s not going to be efficient. The best thing you can do right now is use filter_intervals:
locus = hl.parse_locus('1:10000') mt_filtered = hl.filter_intervals(mt, [hl.interval(locus, locus, includes_start=True, includes_end=True)]) mt_filtered = mt_filtered.filter_cols(mt_filtered.s == 'NA12878') sample_gt = mt_filtered.GT.collect()
All right, thank you very much