PGT

bpblanken · bpblanken · commit 07c60299f326 · 2024-01-15T12:30:19.000-05:00
diff --git a/v03_pipeline/lib/misc/io.py b/v03_pipeline/lib/misc/io.py
@@ -112,8 +112,9 @@ def import_vcf(
         skip_invalid_loci=True,
         contig_recoding=reference_genome.contig_recoding(),
         force_bgz=True,
-        find_replace=('nul', '.'),
+        find_replace=('nul', '.'), # Required for internal exome callsets (+ some AnVIL requests)
         array_elements_required=False,
+        call_fields=[], # PGT is unused downstream, but is occasionally present in old VCFs!
     )
 
 

Original file line number	Diff line number	Diff line change
`@@ -112,8 +112,9 @@ def import_vcf(`
`112`	`112`	`skip_invalid_loci=True,`
`113`	`113`	`contig_recoding=reference_genome.contig_recoding(),`
`114`	`114`	`force_bgz=True,`
`115`		`- find_replace=('nul', '.'),`
	`115`	`+ find_replace=('nul', '.'), # Required for internal exome callsets (+ some AnVIL requests)`
`116`	`116`	`array_elements_required=False,`
	`117`	`+ call_fields=[], # PGT is unused downstream, but is occasionally present in old VCFs!`
`117`	`118`	`)`
`118`	`119`
`119`	`120`