Handle mito correctly

bpblanken · bpblanken · commit ab13f4cf8ab6 · 2024-11-27T12:02:39.000-05:00
diff --git a/v03_pipeline/lib/reference_datasets/misc.py b/v03_pipeline/lib/reference_datasets/misc.py
@@ -109,7 +109,7 @@ def key_by_locus_alleles(ht: hl.Table, reference_genome: ReferenceGenome) -> hl.
     chrom = (
         hl.format('chr%s', ht.chrom)
         if reference_genome == ReferenceGenome.GRCh38
-        else ht.chrom
+        else hl.if_else(ht.chrom == 'M', 'MT', ht.chrom)
     )
     ht = ht.transmute(
         locus=hl.locus(chrom, ht.pos, reference_genome.value),

Original file line number	Diff line number	Diff line change
`@@ -109,7 +109,7 @@ def key_by_locus_alleles(ht: hl.Table, reference_genome: ReferenceGenome) -> hl.`
`109`	`109`	`chrom = (`
`110`	`110`	`hl.format('chr%s', ht.chrom)`
`111`	`111`	`if reference_genome == ReferenceGenome.GRCh38`
`112`		`- else ht.chrom`
	`112`	`+ else hl.if_else(ht.chrom == 'M', 'MT', ht.chrom)`
`113`	`113`	`)`
`114`	`114`	`ht = ht.transmute(`
`115`	`115`	`locus=hl.locus(chrom, ht.pos, reference_genome.value),`