docs(preprocessor): add back descriptions about --missing-to-ref

PharmGKB · Nov 2, 2024 · cacece3 · cacece3
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diff --git a/docs/using/Running-PharmCAT-Pipeline.md b/docs/using/Running-PharmCAT-Pipeline.md
@@ -38,7 +38,7 @@ Standard use case:
 
 ```
 usage: pharmcat_pipeline [-s <samples> | -S <txt_file>]
-                         [--absent-to-ref] [-unspecified-to-ref] [-G] 
+                         [-0] [--absent-to-ref] [-unspecified-to-ref] [-G] 
                          [-R] [-refRegion <bed_file>]
                          [-matcher] [-ma] [-matcherHtml] [-research <type>]
                          [-phenotyper]
@@ -65,9 +65,11 @@ Input arguments:
                         Only applicable if you have multiple samples and only want to work on specific ones.
 
 Preprocessor arguments:
+  -0, --missing-to-ref               
+                        Assume genotypes at absent or unspecified PGx sites are 0/0. This is the combination of `--absent-to-ref` and `-unspecified-to-ref`. DANGEROUS!
   --absent-to-ref             
                         Assume genotypes at absent PGx sites are 0/0.  DANGEROUS!
-  -unspecified-to-ref           
+  --unspecified-to-ref           
                         Assume unspecified genotypes ./. as 0/0 when every sample is './.'. DANGEROUS!
   -G, --no-gvcf-check                
                         Bypass the gVCF check for the input VCF.

diff --git a/docs/using/VCF-Preprocessor.md b/docs/using/VCF-Preprocessor.md
@@ -108,6 +108,13 @@ VCF files can have more than 1 sample and should be [bgzip](http://www.htslib.or
 : Generate 1 VCF file per sample.
 
 
+-0 <span class="altArg"><br />or --missing-to-ref</span>
+: This option will add missing PGx positions to the output. Missing PGx positions are those absent in the input VCF or whose genotypes are unspecified as "./." across all samples. This option is equivalent to the combination of `--absent-to-ref` and `--unspecified-to-ref`. 
+* This option will not convert "./." to "0/0" if any other sample has a specified genotype (`0/0`, `0/1`, etc.) as the unspecified genotypes are likely determined so for good reasons.
+* This **SHOULD ONLY BE USED** if you are sure your data is reference at the absent positions
+instead of being unreadable/uncallable. Running PharmCAT with positions as absent vs reference can lead to different results.
+
+
 --absent-to-ref
 : This option will add absent PGx positions into the output as homozygous reference.
   * This **SHOULD ONLY BE USED** if you are sure your data is reference at the absent positions