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v03_pipeline/migrations/annotations/0004_add_gnomad_svs.py

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@@ -27,11 +27,15 @@ class AddGnomadSVs(BaseMigration):
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@staticmethod
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def migrate(ht: hl.Table, **_) -> hl.Table:
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mapping_ht = hl.import_vcf(
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PHASE_4_CALLSET_WITH_GNOMAD_V4,
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reference_genome=ReferenceGenome.GRCh38.value,
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force_bgz=True
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).key_rows_by('rsid').rows()
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mapping_ht = (
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hl.import_vcf(
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PHASE_4_CALLSET_WITH_GNOMAD_V4,
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reference_genome=ReferenceGenome.GRCh38.value,
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force_bgz=True,
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)
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.key_rows_by('rsid')
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.rows()
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)
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ht = ht.annotate(
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**{
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'info.GNOMAD_V4.1_TRUTH_VID': mapping_ht[ht.key].info[

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