Update StrandBiasBySample documentation (#7283)

This documentation mentions a caveat about not being able to create the annotation with variant annotator, however, users have expressed confusion about not being able to find their StrandBiasBySample (SB) annotations in their final VCFs after using GenotypeGVCFs... which it should not do. There is more information about this on the forum: https://gatk.broadinstitute.org/hc/en-us/community/posts/360077332392-StrandBiasBySample-SB-in-vcf?page=1#community_comment_360015331011 Co-authored-by: ldgauthier <[email protected]>
broadinstitute · Nov 1, 2021 · f31f019 · f31f019
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diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasBySample.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandBiasBySample.java
@@ -43,6 +43,8 @@
  * <h3>Caveats</h3>
  * <ul>
  *     <li>This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator).</li>
+ *     <li>StrandBiasBySample is an intermediate annotation used for calculating FisherStrand (FS) and StrandOddsRatio (SOR), so it will not show up in VCFs after using the GenotypeGVCFs tool
+            unless `--keep-combined-raw-annotations` is specified.</li>
  * </ul>
  *
  * <h3>Related annotations</h3>