Fix compound key in hail #1127
Fix compound key in hail #1127
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## main #1127 +/- ##
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Coverage 26.67% 26.67%
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Files 9 9
Lines 1732 1732
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Hits 462 462
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| # we're using split multiallelics, so we need to compound key on chr/pos/ref/alt | ||
| ht = ht.annotate( | ||
| locus=hl.locus(ht.vep.seq_region_name, hl.parse_int(ht.vep.input.split('\t')[1])), | ||
| alleles=ht.vep.allele_string.split('/'), |
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Is it easy to make this split on '/' OR '|'
Given our push to LR we are going to start seeing phased VCFs more and more so it would be good to build that into our muscle memory
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A split on one of two different separators isn't explicitly available as a hail method, but we can do a replace for | -> /, then split on the latter 🤔
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Not a bit deal for this PR in particular - just one of those footguns that makes me nervous about basic string parsing a VCF.
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I'll bookmark this and have a look for some phased calls in the final MT. I think this might be fine as this is the Alleles string, but the phasing is in the GT field. I would expect that even for 0|1 the alleles being passed to VEP are still in A/T format, with the option of being A/C/T for multiallelics
Correction to #1125
VEP outputs don't have REF/ALF alleles as individual attributes, they only have them within the larger input string, so we need to do some string manipulation to get them
See https://github.com/populationgenomics/production-pipelines/pull/602/files#r1936638900
I previously addressed these issues in a concept PR/branch for making seqr_loader consistently normalise/split multiallelic variants 😅