diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile
index 41df894298f4..49a990d3f216 100644
--- a/biology/gatk/Makefile
+++ b/biology/gatk/Makefile
@@ -1,125 +1,125 @@
 PORTNAME=	gatk
-DISTVERSION=	4.6.1.0
-PORTREVISION=	1
+DISTVERSION=	4.6.2.0
 CATEGORIES=	biology java
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Genome Analysis Toolkit
 WWW=		https://gatk.broadinstitute.org/hc/en-us \
 		https://github.com/broadinstitute/gatk
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.TXT
 
 BUILD_DEPENDS=	gradle8:devel/gradle8
 RUN_DEPENDS=	${LOCALBASE}/lib/libfml.so:biology/fermi-lite \
 		gkl>0:biology/gkl \
 		mummer>0:biology/mummer
 
 USES=		gettext-runtime java python:test
 JAVA_VERSION=	17 # Java 8 fails on aarch64: Internal Error (assembler_aarch64.hpp:237), pid=76025, tid=0x000000000006e359 guarantee(val < (1U << nbits)) failed: Field too big for insn
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	broadinstitute
 
 SUB_FILES=	${PORTNAME}.sh
 SUB_LIST=	PORTVERSION=${PORTVERSION} JAVA=${JAVA}
 
 NO_ARCH=	yes
 
 DEPS_CACHE_DIR=	${WRKDIR}
 
 TEST_ENV=	${MAKE_ENV} \
-		JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \
+		JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so -DLIBFML_PATH=${PREFIX}/lib/libfml.so" \
 		GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
 
 PLIST_FILES=	bin/${PORTNAME} \
 		${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
 
 BINARY_ALIAS=	java=${JAVA} \
 		python=${PYTHON_CMD}
 
 # to rebuild the deps archive:
 #   1. set DEV_UPDATE_MODE=yes
 #   2. make makesum build
 #   3. upload the *-deps archive
 #   4. set DEV_UPDATE_MODE=no
 #   5. make clean makesum
 
 DEV_UPDATE_MODE=	no
 
 OPTIONS_DEFINE=			WITH_LARGE_FILES
 OPTIONS_DEFAULT=		WITH_LARGE_FILES # runtime requires large files, see the README
 
 WITH_LARGE_FILES_DESC=		Download large LFS files needed for build and tests
 WITH_LARGE_FILES_FETCH_DEPENDS=	git:devel/git \
 				git-lfs:devel/git-lfs
 
 # The large files under src/main/resources/large/ are required to build GATK, since they are packaged inside the GATK jar and used by tools at runtime. These are things like ML models and native C/C++ libraries used for acceleration of certain tools.
 # The large files under src/test/resources/large/, on the other hand, are only required by the test suite when running tests.
 
 .include <bsd.port.options.mk>
 
 .if ${PORT_OPTIONS:MWITH_LARGE_FILES}
 # fetch the main distfile including git-lsf files
 do-fetch:
 	@if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \
 		${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \
 		cd ${DISTDIR}/${DIST_SUBDIR} && \
 		${ECHO} "==> Fetching ${PORTNAME} including large LFS files" && \
 		( \
 			${MKDIR} ${WRKDIR}; \
 			HOME=${WRKDIR}; \
 			git config --global filter.lfs.smudge "git-lfs smudge -- %f" && \
 			GIT_CLONE_PROTECTION_ACTIVE=false git clone -nq https://github.com/broadinstitute/gatk.git ${PORTNAME}-${DISTVERSION} && \
 			(cd ${PORTNAME}-${DISTVERSION} && git reset -q --hard ${DISTVERSION} && ${RM} -r .git) && \
 			${RM} -r ${WRKDIR} \
 		) && \
 		${FIND} ${PORTNAME}-${DISTVERSION} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \
 		${FIND} ${PORTNAME}-${DISTVERSION} -print0 | LC_ALL=C ${SORT} -z | \
 		${SETENV} -i ${TAR} czf ${DISTNAME}${EXTRACT_SUFX} --format=cpio --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \
 		${RM} -r ${PORTNAME}-${DISTVERSION}; \
 	fi
 # fetch the deps distfile
 .  if (${DEV_UPDATE_MODE} == "no")
 	@if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" ]; then \
 		${ECHO} "==> Fetching the deps distfile for ${PORTNAME}" && \
 		${SETENV} \
 			${_DO_FETCH_ENV} ${_MASTER_SITES_ENV} \
 			dp_SITE_FLAVOR=MASTER \
 			${SH} ${SCRIPTSDIR}/do-fetch.sh ${DISTFILES:M*\:deps}; \
 	fi
 .  endif
 .endif
 
 .if (${DEV_UPDATE_MODE} == "yes")
 post-build:
 	@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
 	@${ECHO} "(!!!) Please upload the gradle deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
 .else
 MASTER_SITES=	LOCAL/yuri/:deps
 DISTFILES=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
 GRADLE_ARGS=	--offline
 
 post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven
 	@cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}
 .endif
 
 do-build:
 	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle8 \
 		--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
 		${GRADLE_ARGS} --build-cache localJar
 
 do-install:
 	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
 	${INSTALL_DATA} ${WRKSRC}/build/libs/gatk-package-1.0-SNAPSHOT-local.jar ${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
 
 do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space
 	@cd ${WRKSRC} && \
-		${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test
+		${SETENV} ${TEST_ENV} gradle8 test
 
-# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940
+# tests as of 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940
+# tests as of 4.6.2.0: 288719 tests completed, 300 failed, 37 skipped
 # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib
 
 .include <bsd.port.mk>
diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo
index 2494dc43dd72..42fbad5e8a91 100644
--- a/biology/gatk/distinfo
+++ b/biology/gatk/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1730356703
-SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad
-SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997
-SHA256 (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 6f840406ce226e202421464e2ae044f3c0bc63da63f245568f8ca1bc7769d378
-SIZE (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 4317548196
+TIMESTAMP = 1756227460
+SHA256 (gatk-4.6.2.0-deps.tar.gz) = c956ec3b6a209b4eaf9c20cb312635498b360aa372f824b33d392aa0ac594a77
+SIZE (gatk-4.6.2.0-deps.tar.gz) = 903933113
+SHA256 (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = c76b61a549f49004a54ae86e88cd8b7a180a3bd2e4a56b1c9185f30971c79866
+SIZE (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = 4318674606
diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in
index d3d5c0f7bf5a..20c6c16d5164 100644
--- a/biology/gatk/files/gatk.sh.in
+++ b/biology/gatk/files/gatk.sh.in
@@ -1,27 +1,27 @@
 #!/bin/sh
 
 export LC_ALL=en_US.UTF-8
 
 MEM_OPTS_SET_BY_USER="no"
 for o in $@; do
   case $o in
     -X* )
       MEM_OPTS_SET_BY_USER="yes"
       ;;
   esac
 done
 
 if [ $MEM_OPTS_SET_BY_USER = "no" ]; then
   # memory options
   physmem_b=$(sysctl -n hw.physmem)
   physmem_mb=$((physmem_b/1024/1024))
   physmem_mb=$((physmem_mb*3/4)) # allow 3/4 of the memory
   #    -Xms<size>        set initial Java heap size
   #    -Xmx<size>        set maximum Java heap size
   MEM_OPTS="-Xms512m -Xmx${physmem_mb}m"
 fi
 
 # execute the command
 # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient)
-JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \
-%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"
+JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \
+%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"