From f5a2256d59ef6aa060146ada8ab73f86470b0cda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6kalp=20=C3=87elik?= <37572619+gokalpcelik@users.noreply.github.com> Date: Fri, 18 Oct 2024 17:23:39 +0300 Subject: [PATCH] Adding small warning messages to not to feed any GVCF files to these tools (#9008) * Adding small warning messages to not to feed any GVCF files to these tools. * Update src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java Co-authored-by: Louis Bergelson * Update src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java Co-authored-by: Louis Bergelson * Update src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java Co-authored-by: Louis Bergelson --------- Co-authored-by: Louis Bergelson --- .../hellbender/tools/walkers/annotator/VariantAnnotator.java | 4 ++-- .../tools/walkers/fasta/FastaAlternateReferenceMaker.java | 1 + .../hellbender/tools/walkers/vqsr/VariantRecalibrator.java | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java index f29676286e0..fcac0673b89 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotator.java @@ -91,8 +91,8 @@ * --expression foo.FILTER * * - *

Caveat

- *

This tool outputs no annotations by default, all annotations/groups must be specified explicitly.

+ *

Caveats

+ *

This tool outputs no annotations by default, all annotations/groups must be specified explicitly. This tool accepts VCF format files only. Using GVCF files as input may result in unexpected behavior.

* *

Special note on RankSumTestAnnotations

*

RankSumAnnotations produced by this tool are not the same as those produced by the HaplotypeCaller. Without the diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java index 2c3b38f0a9d..0406ad861d5 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/FastaAlternateReferenceMaker.java @@ -41,6 +41,7 @@ *

  • If there are multiple variants that start at a site, it chooses one of them randomly.
    • *
  • When there are overlapping indels (but with different start positions) only the first will be chosen.
    • *
  • This tool works only for SNPs and for simple indels (but not for things like complex substitutions).
    • + *
  • This tool works only with VCF files. Using GVCF files as input may result in unexpected behavior.
    • * *

    Input

    diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java index 41e2bcf9526..5b2b44a3f50 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java @@ -140,7 +140,8 @@ *

    Additional notes

    *
      *
    • This tool only accepts a single input variant file unlike earlier version of GATK, which accepted multiple - * input variant files.
      • + * input variant files. + *
    • The input VCF must be genotyped, raw GVCF files will not work correctly.
      • *
    • SNPs and indels must be recalibrated in separate runs, but it is not necessary to separate them into different * files. See the tutorial linked above for an example workflow. Note that mixed records are treated as indels.
      • *