[MINOR] update NEWS and usage page

Author: pd3

NEWS

@@ -8,6 +8,13 @@ Changes affecting specific commands:
     - New experimental plugin for scoring variants and assess site noisiness from a large number of unaffected
       parental samples
 
+* bcftools +trio-dnm2
+
+    - Fix a problem with --strictly-novel option which would neglect the presence of the apparent de novo
+      allele in the father for male offspring
+
+    - Fix a problem with uncallsed mosaic chrX variants in males
+
 
 ## Release 1.21 (12th September 2024)
 

plugins/trio-dnm2.c

@@ -153,6 +153,7 @@ static const char *usage_text(void)
         "   -T, --targets-file FILE         Similar to -R but streams rather than index-jumps\n"
         "       --targets-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"
         "       --no-version                Do not append version and command line to the header\n"
+        "   -W, --write-index[=FMT]         Automatically index the output files [off]\n"
         "\n"
         "General options:\n"
         "   -m, --min-score NUM             Do not add FMT/DNM annotation if the score is smaller than NUM\n"
@@ -181,7 +182,6 @@ static const char *usage_text(void)
         "       --use-NAIVE                 A naive calling model which uses only FMT/GT to determine DNMs\n"
         "       --with-pAD                  Do not use FMT/QS but parental FMT/AD\n"
         "       --with-pPL                  Do not use FMT/QS but parental FMT/PL. Equals to DNG with bugs fixed (more FPs, fewer FNs)\n"
-        "   -W, --write-index[=FMT]         Automatically index the output files [off]\n"
         "\n"
         "Example:\n"
         "   # Annotate VCF with FORMAT/DNM, run for a single trio\n"