Add annotate_allele_info function to utils.annotations
#535
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A couple comments on the docs and a couple questions: This maintains the nonsplit_alleles=ht.old_alleles. Is this used downstream? We dropped this in v3.1 release since it could contain alleles belonging to unreleased samples. Also looks like the ac_group_filter is in this PR too so you may want to merge main in?
gnomad/utils/annotations.py
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| - variant_type - Variant type (snv, indel, multi-snv, multi-indel, or mixed). | ||
| - n_alt_alleles - Total number of alternate alleles observed at variant locus. | ||
| - has_star - True if the variant contains a star allele. | ||
| - allele_type - Allele type (snv, insertion, deletion, or mixed). | ||
| - was_mixed - True if the variant was mixed (i.e. contained both SNVs and indels). | ||
| - nonsplit_alleles - Array of alleles before splitting. |
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Perhaps change the second - to :?
| - variant_type - Variant type (snv, indel, multi-snv, multi-indel, or mixed). | |
| - n_alt_alleles - Total number of alternate alleles observed at variant locus. | |
| - has_star - True if the variant contains a star allele. | |
| - allele_type - Allele type (snv, insertion, deletion, or mixed). | |
| - was_mixed - True if the variant was mixed (i.e. contained both SNVs and indels). | |
| - nonsplit_alleles - Array of alleles before splitting. | |
| - variant_type: Variant type (snv, indel, multi-snv, multi-indel, or mixed). | |
| - n_alt_alleles: Total number of alternate alleles observed at variant locus. | |
| - has_star: True if the variant contains a star allele. | |
| - allele_type: Allele type (snv, insertion, deletion, or mixed). | |
| - was_mixed: True if the variant was mixed (i.e. contained both SNVs and indels). | |
| - nonsplit_alleles: Array of alleles before splitting. |
Also, I'm not sure these are showing up as intended -- https://broadinstitute.github.io/gnomad_methods/api_reference/utils/annotations.html#gnomad.utils.annotations.annotate_freq
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I think this one will, but I changed the note for annotate_freq so it looks better
jkgoodrich
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Yup, I would like to have it on this annotation HT, but removed from the actual release HT |
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Checks should pass after this PR goes in and I merge with main |
… into jg/add_allele_info_function
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