Do not flag paternal genotyping errors as de novo mutations.

Specifically, when father's chrX genotype is 0/1 and mother's 0/0, 0/1 in the child will not be marked as DNM.
samtools · Dec 11, 2023 · 37cf779 · 37cf779
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commit 37cf779
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Showing 3 changed files with 12 additions and 3 deletions.
diff --git a/NEWS b/NEWS
@@ -109,6 +109,11 @@ Changes affecting specific commands:
       substrings to avoid unexpected spurious matches (i.e. internally add ^ and $ to all
       field names)
 
+* bcftools +trio-dnm2
+
+    - Do not flag paternal genotyping errors as de novo mutations. Specifically, when father's
+      chrX genotype is 0/1 and mother's 0/0, 0/1 in the child will not be marked as DNM.
+
 * bcftools view
 
     - Add new `-A, --trim-unseen-allele` option to remove the unseen allele <*> or <NON_REF>

diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c
@@ -567,8 +567,12 @@ static void init_tprob_mprob_chrXX(args_t *args, int fi, int mi, int ci, double
 
     *denovo_allele = ca!=fa && ca!=fb && ca!=ma && ca!=mb ? ca : cb;
 
-    if ( fa!=fb )                   // father cannot be heterozygous in X
-        *mprob = 0, *tprob = 0;
+    if ( fa!=fb )
+    {
+        // this must be a genotype error, father cannot be heterozygous in X; don't flag it as a DNM unless
+        // also autosomal inheritance fails
+        init_tprob_mprob(args,fi,mi,ci,tprob,mprob,denovo_allele);
+    }
     else if ( (ca==fa && (cb==ma||cb==mb)) || (cb==fa && (ca==ma||ca==mb)) )
     {
         if ( ma==mb ) *tprob = 1;

diff --git a/test/trio-dnm/trio-dnm.9.2.out b/test/trio-dnm/trio-dnm.9.2.out
@@ -10,6 +10,6 @@
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