diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index cbdfaa3b607b..64b06bff07e8 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -1,25 +1,25 @@
 PORTNAME=	samtools
-DISTVERSION=	1.15
+DISTVERSION=	1.16.1
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Tools for manipulating next-generation sequencing data
 WWW=		https://www.htslib.org/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
 USES=		autoreconf gmake localbase ncurses perl5 python:env shebangfix
 
 USE_GITHUB=	yes
 
 USE_PERL5=	test
 GNU_CONFIGURE=	yes
 SHEBANG_FILES=	misc/*.pl misc/plot-bamstats test/test.pl
 
 TEST_TARGET=	test
 
 .include <bsd.port.mk>
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 19439fbc44f5..d0c7b4cbb765 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1645831653
-SHA256 (samtools-samtools-1.15_GH0.tar.gz) = 5109a17f221b36291e4bc3ad68a00c28515d4f20a16b4e23806055661ca0df31
-SIZE (samtools-samtools-1.15_GH0.tar.gz) = 4970205
+TIMESTAMP = 1672094602
+SHA256 (samtools-samtools-1.16.1_GH0.tar.gz) = 70a7f358088929272d8c22d6063290ac8420f5351fba237a99fe17851a45d8be
+SIZE (samtools-samtools-1.16.1_GH0.tar.gz) = 4992787
diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist
index aafc040158e0..1d228254f042 100644
--- a/biology/samtools/pkg-plist
+++ b/biology/samtools/pkg-plist
@@ -1,61 +1,62 @@
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
 bin/export2sam.pl
 bin/fasta-sanitize.pl
 bin/interpolate_sam.pl
 bin/maq2sam-long
 bin/maq2sam-short
 bin/md5fa
 bin/md5sum-lite
 bin/novo2sam.pl
 bin/plot-ampliconstats
 bin/plot-bamstats
 bin/psl2sam.pl
 bin/sam2vcf.pl
 bin/samtools
 bin/samtools.pl
 bin/seq_cache_populate.pl
 bin/soap2sam.pl
 bin/wgsim
 bin/wgsim_eval.pl
 bin/zoom2sam.pl
 man/man1/samtools-addreplacerg.1.gz
 man/man1/samtools-ampliconclip.1.gz
 man/man1/samtools-ampliconstats.1.gz
 man/man1/samtools-bedcov.1.gz
 man/man1/samtools-calmd.1.gz
 man/man1/samtools-cat.1.gz
 man/man1/samtools-collate.1.gz
 man/man1/samtools-consensus.1.gz
 man/man1/samtools-coverage.1.gz
 man/man1/samtools-depad.1.gz
 man/man1/samtools-depth.1.gz
 man/man1/samtools-dict.1.gz
 man/man1/samtools-faidx.1.gz
 man/man1/samtools-fasta.1.gz
 man/man1/samtools-fastq.1.gz
 man/man1/samtools-fixmate.1.gz
 man/man1/samtools-flags.1.gz
 man/man1/samtools-flagstat.1.gz
 man/man1/samtools-fqidx.1.gz
 man/man1/samtools-head.1.gz
 man/man1/samtools-idxstats.1.gz
 man/man1/samtools-import.1.gz
 man/man1/samtools-index.1.gz
 man/man1/samtools-markdup.1.gz
 man/man1/samtools-merge.1.gz
 man/man1/samtools-mpileup.1.gz
 man/man1/samtools-phase.1.gz
 man/man1/samtools-quickcheck.1.gz
+man/man1/samtools-reference.1.gz
 man/man1/samtools-reheader.1.gz
 man/man1/samtools-rmdup.1.gz
 man/man1/samtools-samples.1.gz
 man/man1/samtools-sort.1.gz
 man/man1/samtools-split.1.gz
 man/man1/samtools-stats.1.gz
 man/man1/samtools-targetcut.1.gz
 man/man1/samtools-tview.1.gz
 man/man1/samtools-view.1.gz
 man/man1/samtools.1.gz
 man/man1/wgsim.1.gz