diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index 8e45ca34e041..964affb3cd6f 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	bcftools
-PORTVERSION=	1.10.2
+PORTVERSION=	1.11
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -13,6 +13,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 LIB_DEPENDS=	libhts.so.3:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
+RUN_DEPENDS=	bash:shells/bash
 
 USES=		autoreconf gmake localbase perl5 python:env shebangfix
 
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index 9e0401b10cfd..aac1660e88f1 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1595166811
-SHA256 (samtools-bcftools-1.10.2_GH0.tar.gz) = 13277c17047152951e0bfe4467adc7768571b18e26610d206cab5560de5a395a
-SIZE (samtools-bcftools-1.10.2_GH0.tar.gz) = 2880994
+TIMESTAMP = 1603028344
+SHA256 (samtools-bcftools-1.11_GH0.tar.gz) = f2d9a09fd7920754b60948b81ec047882864213b93a0cd1ef0372b0e025cba3f
+SIZE (samtools-bcftools-1.11_GH0.tar.gz) = 3004923
diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile
index b44cd69acd3e..8dc6a8e96e69 100644
--- a/biology/bcftools/files/patch-Makefile
+++ b/biology/bcftools/files/patch-Makefile
@@ -1,26 +1,6 @@
---- Makefile.orig	2019-12-19 09:57:32 UTC
+--- Makefile.orig	2020-10-18 13:31:52 UTC
 +++ Makefile
-@@ -22,13 +22,12 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--AR       = ar
--RANLIB   = ranlib
--CPPFLAGS =
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
--LIBS     =
-+CC       ?= gcc
-+AR       ?= ar
-+RANLIB   ?= ranlib
-+CPPFLAGS ?=
-+CFLAGS   ?= -g -Wall -O2
-+LDFLAGS  ?=
- 
- DYNAMIC_FLAGS = -rdynamic
- PLUGINS_ENABLED = yes
-@@ -45,7 +44,8 @@ OBJS     = main.o vcfindex.o tabix.o \
+@@ -45,7 +45,8 @@ OBJS     = main.o vcfindex.o tabix.o \
             ccall.o em.o prob1.o kmin.o # the original samtools calling
  PLUGIN_OBJS = vcfplugin.o
  
@@ -30,18 +10,20 @@
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  libdir      = $(exec_prefix)/lib
-@@ -58,13 +58,13 @@ pluginpath  = $(plugindir)
+@@ -58,13 +59,14 @@ pluginpath  = $(plugindir)
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
  misc_bindir = $(bindir)
  
-+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
- MKDIR_P = mkdir -p
+-MKDIR_P = mkdir -p
 -INSTALL = install -p
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
 -INSTALL_MAN     = $(INSTALL_DATA)
 -INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
++MKDIR_P 	= mkdir -p
++INSTALL 	= install -p
 +INSTALL_DATA    = ${BSD_INSTALL_DATA}
 +INSTALL_DIR     = $(MKDIR_P)
 +INSTALL_MAN     = ${BSD_INSTALL_MAN}
@@ -50,7 +32,7 @@
  
  PROGRAMS = bcftools
  MISC_SCRIPTS = \
-@@ -141,7 +141,7 @@ print-version:
+@@ -142,7 +144,7 @@ print-version:
  ifdef USE_GPL
      main.o : EXTRA_CPPFLAGS += -DUSE_GPL
      OBJS += polysomy.o peakfit.o
@@ -59,12 +41,3 @@
  endif
  
  print-%:
-@@ -320,7 +320,7 @@ docs: doc/bcftools.1 doc/bcftools.html
- # Since there is no make dependency, bcftools.1 can be out-of-date and
- # make docs can be run to update if asciidoc is available
- install: $(PROGRAMS) $(PLUGINS)
--	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
-+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
- 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
- 	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
- 	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
diff --git a/biology/bcftools/files/patch-misc_run-roh.pl b/biology/bcftools/files/patch-misc_run-roh.pl
deleted file mode 100644
index 4b5cd6200284..000000000000
--- a/biology/bcftools/files/patch-misc_run-roh.pl
+++ /dev/null
@@ -1,11 +0,0 @@
---- misc/run-roh.pl.orig	2017-10-18 09:33:24 UTC
-+++ misc/run-roh.pl
-@@ -97,7 +97,7 @@ sub cmd
-     else 
-     {      
-         # child
--        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
-+        exec('/bin/sh', '-c', $cmd) or error("Failed to run the command [/bin/sh -c $cmd]: $!");
-     }
- 
-     if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }
diff --git a/biology/bcftools/files/patch-test_test.pl b/biology/bcftools/files/patch-test_test.pl
index 079f0e7fe78b..39ccb4466b54 100644
--- a/biology/bcftools/files/patch-test_test.pl
+++ b/biology/bcftools/files/patch-test_test.pl
@@ -1,24 +1,6 @@
---- test/test.pl.orig	2020-07-21 20:49:56 UTC
+--- test/test.pl.orig	2020-10-18 13:36:42 UTC
 +++ test/test.pl
-@@ -610,7 +610,7 @@ sub _cmd
-     else
-     {
-         # child
--        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
-+        exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!");
-     }
-     return ($? >> 8, join('',@out));
- }
-@@ -622,7 +622,7 @@ sub _cmd3
-     my $pid = fork();
-     if ( !$pid )
-     {
--        exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
-+        exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
-     }
-     waitpid($pid,0);
- 
-@@ -1063,7 +1063,7 @@ sub test_usage
+@@ -1236,7 +1236,7 @@ sub test_usage
      my $command = $args{cmd};
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
@@ -27,7 +9,7 @@
  
      my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
  
-@@ -1118,7 +1118,7 @@ sub test_usage_subcommand
+@@ -1291,7 +1291,7 @@ sub test_usage_subcommand
      my $subcommand = $args{subcmd};
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist
index cc32e1b8aa50..ed393533217b 100644
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@@ -1,5 +1,6 @@
 bin/bcftools
 bin/color-chrs
+bin/gff2gff.py
 bin/guess-ploidy
 bin/plot-roh
 bin/plot-vcfstats
@@ -33,6 +34,7 @@ libexec/bcftools/missing2ref.so
 libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
 libexec/bcftools/remove-overlaps.so
+libexec/bcftools/scatter.so
 libexec/bcftools/setGT.so
 libexec/bcftools/smpl-stats.so
 libexec/bcftools/split-vep.so