Indel matching in semi_join/anti_join

Science
1

Hi

I am using semi_join(), anti_join(), semi_join_rows() and anti_join_rows() to discover variants which are present in both of two datasets, or variants present in only one dataset.
I have a question about indel normalisation. Does Hail either left-align or normalise indels when running these functions?
i.e. will it recognise something like chr1:119753410 AACAC>AAC and chr1:119753412 CAC>C as being the same variant? Or if faced with two different representations of the same indel will it consider them as different variants?

Many thanks in advance

Ruth

2

Hail doesn’t automatically compute the minimal representation of indels when you join. It’s certainly possible to do this yourself:

mt = mt.key_rows_by(**hl.min_rep(mt.locus, mt.alleles))

ht = ht.key_by(**hl.min_rep(ht.locus, ht.alleles))
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3

Thank you, that is very helpful :+1: