From 05c9c5cdb7e64dd46648a3531d6bdc8347c8d6c4 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Mon, 26 Jun 2023 09:18:20 -0500 Subject: [PATCH] Update proximal_vcf.rst to mention GATK 3.6.0 --- docs/pvacseq/input_file_prep/proximal_vcf.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/pvacseq/input_file_prep/proximal_vcf.rst b/docs/pvacseq/input_file_prep/proximal_vcf.rst index 2e72c42d9..6ad3c4453 100644 --- a/docs/pvacseq/input_file_prep/proximal_vcf.rst +++ b/docs/pvacseq/input_file_prep/proximal_vcf.rst @@ -110,6 +110,8 @@ ______________________________ Phase variants using GATK’s ReadBackedPhasing _____________________________________________ +Unfortunately, the tool used for this step is no longer available in current versions of GATK. We recommend using GATK 3.6.0 to run this step. + .. code-block:: none /usr/bin/java -Xmx16g -jar /opt/GenomeAnalysisTK.jar \