Output missing FORMAT/VAF values in non-trio samples, rather than random nonsense values

Author: pd3

NEWS

@@ -133,6 +133,8 @@ Changes affecting specific commands:
     - Allow to set the `--pn` and `--pns` options separately for SNVs and indels and make
       the indel settings more strict by default
 
+    - Output missing FORMAT/VAF values in non-trio samples, rather than random nonsense values
+
 * bcftools +variant-distance
 
     - New option `-d, --direction` to choose the directionality: forward, reverse, nearest (the default)

plugins/trio-dnm2.c

@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2018-2022 Genome Research Ltd.
+   Copyright (c) 2018-2023 Genome Research Ltd.
 
    Author: Petr Danecek <[email protected]>
 
@@ -1375,6 +1375,7 @@ static void process_record(args_t *args, bcf1_t *rec)
     else
         for (i=0; i<nsmpl; i++) args->dnm_qual_int[i] = bcf_int32_missing;
     for (i=0; i<nsmpl; i++) args->dnm_allele[i] = bcf_int32_missing;
+    for (i=0; i<nsmpl; i++) args->vaf[i] = bcf_int32_missing;
     for (i=0; i<args->ntrio; i++)
     {
         if ( args->filter && !args->trio[i].pass ) continue;