diff --git a/Makefile b/Makefile
index 2b6401b8..4dbc8ea0 100644
--- a/Makefile
+++ b/Makefile
@@ -40,7 +40,7 @@ install-pgip: ## Create pgip environment and install packages to render site
 	if conda env list | cut -f1 -d ' ' | grep -q "${PGIP}$$"; then \
 		echo "Environment exists; skipping install"; \
 	else \
-		mamba env create -n ${PGIP} --file environment.yml; \
+		mamba env create -n ${PGIP} conda-linux-64.lock; \
 	fi;
 
 install-dev: install-pgip ## Install additional development tools
@@ -48,8 +48,8 @@ install-dev: install-pgip ## Install additional development tools
 
 install-R: install-pgip ## Install additional R packages that require manual installation
 	R -e "install.packages('dotenv', repos=c(CRAN = 'https://cran.rstudio.com/'))"
-	R -e "tinytex::tlmgr_update()"
-	R -e "tinytex::reinstall_tinytex(force=TRUE)"
+	#R -e "tinytex::tlmgr_update()"
+	#R -e "tinytex::reinstall_tinytex(force=TRUE)"
 	R -e "library(devtools); devtools::install_local('src/R/pgip')"
 
 install-kernels: install-pgip ## Install python and bash kernel
diff --git a/README.md b/README.md
index 33287b2f..b89fda66 100644
--- a/README.md
+++ b/README.md
@@ -58,7 +58,6 @@ environment variable:
     conda activate pgip
     make install-R
     make install-kernels
-    make install-bcftools
     make install-pixy
     make install-dev
 
@@ -73,9 +72,9 @@ issues](#installation-issues).
 
 ### Create pgip conda environment
 
-Create a conda environment called `pgip` using the environment file
+Create a conda environment called `pgip` using the conda lock file
 
-    mamba env create --file environment.yml
+    mamba env create -n pgip conda-linux-64.lock
 
 and activate the environment
 
@@ -123,7 +122,10 @@ information.
 
 [Install Quarto](https://quarto.org/docs/get-started) version [Quarto\>=1.2.475](https://quarto.org/docs/download/).
 
-### bcftools manual install
+### bcftools manual install (OBSOLETE)
+
+**OBSOLETE**: installing pgip using `conda-linux-64.lock` obviates the
+need to install bcftools manually.
 
 Due to dependency issues, bcftools has to be manually installed:
 
diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 7ef4be78..448e5518 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 330a9f5379ba2437f05fb5dc5c8049e7125179b9d9dbd17d3574bf694145cf33
+# input_hash: ccdee737e20be468134c47f3360b338b90dc2155ded7397103a65a5e4474a8e3
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
@@ -28,6 +28,7 @@ https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
 https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2#be733e69048951df1e4b4b7bb8c7666f
 https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.8.5-h166bdaf_0.tar.bz2#5590453a8d072c9c89bfa26fcf88d870
+https://conda.anaconda.org/conda-forge/linux-64/bc-1.07.1-h7f98852_0.tar.bz2#9ff50d162aa3b1c861fa30105bea1932
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.20.1-hd590300_1.conda#2facbaf5ee1a56967aecaee89799160e
 https://conda.anaconda.org/conda-forge/linux-64/freexl-1.0.6-h166bdaf_1.tar.bz2#897e772a157faf3330d72dd291486f62
@@ -68,6 +69,7 @@ https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318
 https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
 https://conda.anaconda.org/conda-forge/linux-64/nspr-4.35-h27087fc_0.conda#da0ec11a6454ae19bff5b02ed881a2b1
+https://conda.anaconda.org/conda-forge/linux-64/oniguruma-6.9.9-hd590300_0.conda#77dab674d16c1525ebe65e67de30de0d
 https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1w-hd590300_0.conda#301e70057a3bd399640bb16bbdf87995
 https://conda.anaconda.org/conda-forge/linux-64/pixman-0.42.2-h59595ed_0.conda#700edd63ccd5fc66b70b1c028cea9a68
 https://conda.anaconda.org/conda-forge/linux-64/pkg-config-0.29.2-h36c2ea0_1008.tar.bz2#fbef41ff6a4c8140c30057466a1cdd47
@@ -102,6 +104,7 @@ https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9
 https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.2.0-h338b0a0_2.conda#b4f2ab4faf22658cca303570fd9a7662
 https://conda.anaconda.org/conda-forge/linux-64/glog-0.6.0-h6f12383_0.tar.bz2#b31f3565cb84435407594e548a2fb7b2
 https://conda.anaconda.org/conda-forge/linux-64/glpk-5.0-h445213a_0.tar.bz2#efc4b0c33bdf47312ad5a8a0587fa653
+https://conda.anaconda.org/conda-forge/linux-64/jq-1.6-h36c2ea0_1000.tar.bz2#8578ae83310b8c9f5717f1aa65054f36
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.0.9-h166bdaf_9.conda#081aa22f4581c08e4372b0b6c2f8478e
 https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_9.conda#1f0a03af852a9659ed2bf08f2f1704fd
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
@@ -135,6 +138,7 @@ https://conda.anaconda.org/conda-forge/linux-64/bgen-4.1.3-ha0ad84f_0.tar.bz2#bd
 https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.5-h0f2a231_0.conda#009521b7ed97cca25f8f997f9e745976
 https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.78.0-h5adbc97_2.conda#09be6b4c66c7881e2b24214c6f6841c9
 https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.0.9-h166bdaf_9.conda#d47dee1856d9cb955b8076eeff304a5b
+https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.17-he4a0461_11.tar.bz2#23832bbbdfb4a2c05e2df120068b1c78
 https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.9.14-ha770c72_1.tar.bz2#5746d6202ba2abad4a4707f2a2462795
 https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hc118613_108.conda#6fa90698000b05dfe8ce6515794fe71a
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
@@ -159,6 +163,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tktable-2.10-h0c5db8f_5.conda#94
 https://conda.anaconda.org/bioconda/linux-64/vcftools-0.1.16-pl5321hdcf5f25_9.tar.bz2#f397124fda8a7eba9ab6d1326b3f1ee3
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.4-h0b41bf4_0.conda#ea8fbfeb976ac49cbeb594e985393514
 https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2#5f095bc6454094e96f146491fd03633b
+https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.1.2-pyhd8ed1ab_0.conda#05718204d3570baccbda39c830bbe4d9
 https://conda.anaconda.org/conda-forge/noarch/asciitree-0.3.3-py_2.tar.bz2#c0481c9de49f040272556e2cedf42816
 https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-hd4edc92_1.tar.bz2#6c72ec3e660a51736913ef6ea68c454b
 https://conda.anaconda.org/conda-forge/noarch/attrs-23.1.0-pyh71513ae_1.conda#3edfead7cedd1ab4400a6c588f3e75f8
@@ -255,10 +260,12 @@ https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.5-pyhd8ed1ab_1.conda#3
 https://conda.anaconda.org/conda-forge/noarch/tabulate-0.9.0-pyhd8ed1ab_1.tar.bz2#4759805cce2d914c38472f70bf4d8bcb
 https://conda.anaconda.org/conda-forge/noarch/tblib-2.0.0-pyhd8ed1ab_0.conda#f5580336fe091d46f9a2ea97da044550
 https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.2.0-pyha21a80b_0.conda#978d03388b62173b8e6f79162cf52b86
+https://conda.anaconda.org/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_0.tar.bz2#f832c45a477c78bebd107098db465095
 https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96
+https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.12.1-pyha770c72_0.conda#62f5b331c53d73e2f6c4c130b53518a0
 https://conda.anaconda.org/conda-forge/noarch/toolz-0.12.0-pyhd8ed1ab_0.tar.bz2#92facfec94bc02d6ccf42e7173831a36
 https://conda.anaconda.org/conda-forge/linux-64/tornado-6.3.3-py310h2372a71_1.conda#b23e0147fa5f7a9380e06334c7266ad5
-https://conda.anaconda.org/conda-forge/noarch/traitlets-5.11.2-pyhd8ed1ab_0.conda#bd3f90f7551e1cffb1f402880eb2cef1
+https://conda.anaconda.org/conda-forge/noarch/traitlets-5.12.0-pyhd8ed1ab_0.conda#3ecde21191a20e0e4ab5a4d69aaaa22c
 https://conda.anaconda.org/conda-forge/noarch/types-python-dateutil-2.8.19.14-pyhd8ed1ab_0.conda#4df15c51a543e806d439490b862be1c6
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.8.0-pyha770c72_0.conda#5b1be40a26d10a06f6d4f1f9e19fa0c7
 https://conda.anaconda.org/conda-forge/noarch/typing_utils-0.1.0-pyhd8ed1ab_0.tar.bz2#eb67e3cace64c66233e2d35949e20f92
@@ -269,6 +276,7 @@ https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_2.co
 https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.6.4-pyhd8ed1ab_0.conda#bdb77b28cf16deac0eef431a068320e8
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.2-pyhd8ed1ab_0.conda#1ccd092478b3e0ee10d7a891adbf8a4f
 https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.9-pyhd8ed1ab_0.conda#82617d07b2f5f5a96296d3c19684b37a
+https://conda.anaconda.org/conda-forge/noarch/xmltodict-0.13.0-pyhd8ed1ab_0.tar.bz2#b5b33faed6ed2b4ba47a690b8f5c0818
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h7f98852_1003.tar.bz2#f59c1242cc1dd93e72c2ee2b360979eb
@@ -281,7 +289,7 @@ https://conda.anaconda.org/conda-forge/noarch/asttokens-2.4.0-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/async-lru-2.0.4-pyhd8ed1ab_0.conda#3d081de3a6ea9f894bbb585e8e3a4dcb
 https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.6.21-hd93a3ba_3.conda#1dc0c00522a7251d739d46b03637fce5
 https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.7.13-h0b5698f_12.conda#a1b44dfb2c581a9d74c4fdf826d66d6a
-https://conda.anaconda.org/conda-forge/noarch/babel-2.13.0-pyhd8ed1ab_0.conda#22541af7a9eb59fc6afcadb7ecdf9219
+https://conda.anaconda.org/conda-forge/noarch/babel-2.13.1-pyhd8ed1ab_0.conda#3ccff479c246692468f604df9c85ef26
 https://conda.anaconda.org/conda-forge/noarch/backports.functools_lru_cache-1.6.5-pyhd8ed1ab_0.conda#6b1b907661838a75d067a22f87996b2e
 https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.12.2-pyha770c72_0.conda#a362ff7d976217f8fa78c0f1c4f59717
 https://conda.anaconda.org/conda-forge/noarch/bleach-6.1.0-pyhd8ed1ab_0.conda#0ed9d7c0e9afa7c025807a9a8136ea3e
@@ -317,12 +325,12 @@ https://conda.anaconda.org/conda-forge/linux-64/pillow-9.4.0-py310h023d228_1.con
 https://conda.anaconda.org/conda-forge/noarch/pip-23.3.1-pyhd8ed1ab_0.conda#2400c0b86889f43aa52067161e1fb108
 https://conda.anaconda.org/conda-forge/linux-64/postgresql-15.1-h84e8d4a_3.conda#d2c2625f20744ca8ace433cb0c01d043
 https://conda.anaconda.org/conda-forge/linux-64/proj-9.1.0-h8ffa02c_1.conda#ed901e1f5c504b144b31f015c6702634
-https://conda.anaconda.org/conda-forge/noarch/pytest-7.4.2-pyhd8ed1ab_0.conda#6dd662ff5ac9a783e5c940ce9f3fe649
+https://conda.anaconda.org/conda-forge/noarch/pytest-7.4.3-pyhd8ed1ab_0.conda#5bdca0aca30b0ee62bb84854e027eae0
 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984
-https://conda.anaconda.org/conda-forge/noarch/qtpy-2.4.0-pyhd8ed1ab_0.conda#a4c1fc5f8ef46ec8130defcaa2d322ea
+https://conda.anaconda.org/conda-forge/noarch/qtpy-2.4.1-pyhd8ed1ab_0.conda#7f391bd70d2abfb70f304ba5aa4e1261
 https://conda.anaconda.org/conda-forge/noarch/referencing-0.30.2-pyhd8ed1ab_0.conda#a33161b983172ba6ef69d5fc850650cd
 https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab_0.tar.bz2#fed45fc5ea0813240707998abe49f520
-https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml-0.17.39-py310h2372a71_0.conda#7e10c23928a18d055177d33877b9b533
+https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml-0.18.2-py310h2372a71_0.conda#01a71da7d9db1108a832ad7e04b8f824
 https://conda.anaconda.org/conda-forge/noarch/svgwrite-1.4.3-pyhd8ed1ab_0.tar.bz2#9d1eb6e4bf36cf72e0662ed9246f4e1b
 https://conda.anaconda.org/conda-forge/noarch/sympy-1.12-pypyh9d50eac_103.conda#2f7d6347d7acf6edf1ac7f2189f44c8f
 https://conda.anaconda.org/conda-forge/noarch/terminado-0.17.1-pyh41d4057_0.conda#3788984d535770cad699efaeb6cb3037
@@ -333,6 +341,7 @@ https://conda.anaconda.org/conda-forge/noarch/urllib3-2.0.7-pyhd8ed1ab_0.conda#2
 https://conda.anaconda.org/conda-forge/linux-64/xerces-c-3.2.4-h55805fa_1.tar.bz2#d127dc8efe24033b306180939e51e6af
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h7f98852_0.tar.bz2#e77615e5141cad5a2acaa043d1cf0ca5
 https://conda.anaconda.org/conda-forge/linux-64/yarl-1.9.2-py310h2372a71_1.conda#30ae8a8f248b4e7cd2622cff41cb05a7
+https://conda.anaconda.org/conda-forge/noarch/yq-3.2.3-pyhd8ed1ab_0.conda#15d2d46390b69750282c11c1e1438b2f
 https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py310h2372a71_4.conda#68ee85860502d53c8cbfa0e4cef0f6cb
 https://conda.anaconda.org/conda-forge/noarch/arrow-1.3.0-pyhd8ed1ab_0.conda#b77d8c2313158e6e461ca0efb1c2c508
 https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.2.1-h5d7e488_4.conda#9e8136470128515530b8cc0b53720084
@@ -384,6 +393,7 @@ https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.39-pyha770c72_0
 https://conda.anaconda.org/conda-forge/linux-64/pytorch-2.0.0-cpu_generic_py310h7ffd2bf_1.conda#a0b9af67d9386330f983a8a3d5da9660
 https://conda.anaconda.org/conda-forge/noarch/rich-click-1.7.0-pyhd8ed1ab_0.conda#564af8d7ea5992556df52e4da16f2719
 https://conda.anaconda.org/conda-forge/linux-64/scipy-1.11.3-py310hb13e2d6_1.conda#4260b359d8fbeab4f789a8b0f968079f
+https://conda.anaconda.org/bioconda/linux-64/tabixpp-1.1.0-h468462d_10.tar.bz2#8c427983c96e65ec4ac4fbc1228c6be2
 https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.9.379-h56135f1_7.conda#359811ce2b6ca67a19dbb818dd83f1c6
 https://conda.anaconda.org/conda-forge/linux-64/bed-reader-0.2.36-py310h93aa1c4_2.conda#4360f85d324866f3750c5761d6171267
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@@ -393,19 +403,23 @@ https://conda.anaconda.org/bioconda/noarch/fastqc-0.12.1-hdfd78af_0.tar.bz2#c9f6
 https://conda.anaconda.org/bioconda/noarch/gatk4-4.4.0.0-py36hdfd78af_0.tar.bz2#ab2bdd8fd02976636a45e229db3de42c
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-https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.4.0-pyhd8ed1ab_0.conda#554496685357ab0d69676cab8e8fb594
+https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.5.0-pyhd8ed1ab_0.conda#77e442cb7c382d01c916f91a8652811a
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 https://conda.anaconda.org/conda-forge/linux-64/r-svglite-2.1.2-r42h329214f_0.conda#8b4d5f45551aa3be5e0b667588b64ddb
@@ -553,6 +586,10 @@ https://conda.anaconda.org/conda-forge/noarch/r-urlchecker-1.0.1-r42hc72bb7e_2.c
 https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.4-r42ha503ecb_0.conda#fdce6d2f939cb678c6eaf743f8c2153e
 https://conda.anaconda.org/conda-forge/noarch/r-xopen-1.0.0-r42hc72bb7e_1005.conda#5a3e7fb0eb2ebd3d3a775f455d03a61f
 https://conda.anaconda.org/conda-forge/linux-64/r-xts-0.13.1-r42h57805ef_1.conda#7848dc64d8e49916f3e85e14f32118d2
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-biocparallel-1.32.5-r42hf17093f_1.tar.bz2#4b8d5c357472319d1ac790f0c1864586
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-delayedarray-0.24.0-r42ha9d7317_1.tar.bz2#5d7d600f0be04e8b7c236171df94b667
+https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodb-1.34.9-r42hdfd78af_0.tar.bz2#10961a4cf078c3e368caa1465a45feca
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.38.0-r42ha9d7317_1.tar.bz2#eb5ece9b227b55a9c20ab165a9f97087
 https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.2.0-pyhd8ed1ab_0.conda#38589f4104d11f2a59ff01a9f4e3bfb3
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda#a52834fa7e3d12abc5efdf06b2097a05
 https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.9.2-pyhd8ed1ab_0.conda#16ccaddfcfa0a1a606a9ecf6a52d6c11
@@ -565,7 +602,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-fontawesome-0.5.2-r42hc72bb7e_0.
 https://conda.anaconda.org/conda-forge/linux-64/r-graphlayouts-1.0.1-r42ha503ecb_0.conda#5d03b055ed25454ca0bc2162b305c9a7
 https://conda.anaconda.org/conda-forge/noarch/r-gridextra-2.3-r42hc72bb7e_1005.conda#da116b29105a8d48571975a185e9bb94
 https://conda.anaconda.org/conda-forge/noarch/r-hms-1.1.3-r42hc72bb7e_1.conda#18275801a3c5f928d7a7da60470f4cc3
-https://conda.anaconda.org/conda-forge/linux-64/r-httpuv-1.6.11-r42ha503ecb_1.conda#60a200fdb55e4d0bb03c1685f4a26d11
+https://conda.anaconda.org/conda-forge/linux-64/r-httpuv-1.6.12-r42ha503ecb_0.conda#ce15e23b165b5888e8c06dfac3fbbb16
 https://conda.anaconda.org/conda-forge/noarch/r-httr-1.4.7-r42hc72bb7e_0.conda#5ea781f852e922b927ed46fa7e188e45
 https://conda.anaconda.org/conda-forge/noarch/r-httr2-0.2.3-r42hc72bb7e_1.conda#b5eb2cf5af14804233cbe583ba3b4d6c
 https://conda.anaconda.org/conda-forge/noarch/r-jquerylib-0.1.4-r42hc72bb7e_2.conda#d748f7b4d48529b0ad0308f0be1dd132
@@ -582,6 +619,8 @@ https://conda.anaconda.org/conda-forge/linux-64/r-tidyselect-1.2.0-r42hc72bb7e_1
 https://conda.anaconda.org/conda-forge/linux-64/r-ttr-0.24.3-r42h57805ef_2.conda#ec5ca53886ef1bf9924d3542ec47dda1
 https://conda.anaconda.org/conda-forge/linux-64/r-tweenr-2.0.2-r42ha503ecb_2.conda#91b9dc22818766dd07b2bd950879ba38
 https://conda.anaconda.org/conda-forge/noarch/r-webshot-0.5.5-r42hc72bb7e_0.conda#55b3514eb941d4f53dc85e675e175962
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-biostrings-2.66.0-r42ha9d7317_1.tar.bz2#42ec86503c7e99250a649a289e42931b
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-genomicranges-1.50.0-r42ha9d7317_1.tar.bz2#cabdf824b390b5a2079139635d357b05
 https://conda.anaconda.org/conda-forge/noarch/dask-2023.10.0-pyhd8ed1ab_0.conda#0c85f5482dd283c2b9ca68d331edb471
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.7-pyhd8ed1ab_0.conda#80318d83f33b3bf4e57b8533b7a6691d
 https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.5.1-r42hc72bb7e_0.conda#69dc8467f9c463a85665c6188b14d683
@@ -594,6 +633,8 @@ https://conda.anaconda.org/conda-forge/noarch/r-quantmod-0.4.25-r42hc72bb7e_0.co
 https://conda.anaconda.org/conda-forge/noarch/r-rcmdcheck-1.4.0-r42h785f33e_2.conda#fae4c087b4ba7bb806ac16475f057156
 https://conda.anaconda.org/conda-forge/noarch/r-selectr-0.4_2-r42hc72bb7e_3.conda#797e58272dca8e284fdd4003cd261d62
 https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r42h57805ef_2.conda#b1278a5148c9e52679bb72112770cdc3
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsamtools-2.14.0-r42hf17093f_1.tar.bz2#ad740ac1090ee2d46bd0a824002fcb25
+https://conda.anaconda.org/bioconda/noarch/bioconductor-summarizedexperiment-1.28.0-r42hdfd78af_0.tar.bz2#3bfc1739950dd7f3f57b35c5ff6d59e7
 https://conda.anaconda.org/conda-forge/noarch/dask-glm-0.2.0-py_1.tar.bz2#7c9c5295a0499bf56bbf084578618af5
 https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.6-pyhd8ed1ab_0.conda#d60881c78a54cbf8042ae719f1f77a50
 https://conda.anaconda.org/conda-forge/noarch/r-cellranger-1.1.0-r42hc72bb7e_1006.conda#dc3d9655cb252f807936ebc9904bf13a
@@ -608,6 +649,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-usethis-2.2.2-r42hc72bb7e_0.cond
 https://conda.anaconda.org/conda-forge/linux-64/r-vroom-1.6.4-r42ha503ecb_0.conda#6af79478af6d212423678c1d6a41c02e
 https://conda.anaconda.org/conda-forge/noarch/rechunker-0.5.0-pyhd8ed1ab_0.tar.bz2#6ba4c5fbad9837929bfcda5c16617214
 https://conda.anaconda.org/conda-forge/linux-64/scikit-allel-1.3.7-py310hcc13569_1.conda#fcce4bf948839c012665c5020dc21edc
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-genomicalignments-1.34.0-r42ha9d7317_1.tar.bz2#17a36626ef7669c2d320797e276f78cb
 https://conda.anaconda.org/conda-forge/noarch/dask-ml-2023.3.24-pyhd8ed1ab_1.conda#24849fcc0f888d2ab326e681ece8b985
 https://conda.anaconda.org/conda-forge/noarch/jupyter-1.0.0-pyhd8ed1ab_10.conda#056b8cc3d9b03f54fc49e6d70d7dc359
 https://conda.anaconda.org/conda-forge/noarch/r-gganimate-1.0.8-r42hc72bb7e_3.conda#5972f9a07e2bcacadd44326f41c1cca5
@@ -623,6 +665,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-readxl-1.4.3-r42ha5c9fba_0.con
 https://conda.anaconda.org/conda-forge/linux-64/r-tidyr-1.3.0-r42ha503ecb_1.conda#19bb60e102c1b3b7e5fb622be2d4f816
 https://conda.anaconda.org/conda-forge/noarch/r-viridis-0.6.4-r42hc72bb7e_0.conda#992866162be83135e6ad2ddf64a13647
 https://conda.anaconda.org/conda-forge/noarch/r-waldo-0.5.1-r42hc72bb7e_1.conda#6cc918319415daeb4ba504f0bd5d21dd
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-rtracklayer-1.58.0-r42h171f361_1.tar.bz2#5de52ab251fc19198d8e50223e59ff8f
 https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.5-r42hc72bb7e_1.conda#c3ad1beca9e00f10a8764473d081b717
 https://conda.anaconda.org/conda-forge/noarch/r-dt-0.28-r42hc72bb7e_1.conda#4e4a5f51e3a68ec93f4ebbab6bee99e9
 https://conda.anaconda.org/conda-forge/noarch/r-dygraphs-1.1.1.6-r42hc72bb7e_1005.conda#710466727f8ce1de3a410314a435b76e
@@ -635,6 +678,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-profvis-0.3.8-r42h57805ef_3.co
 https://conda.anaconda.org/conda-forge/linux-64/r-testthat-3.2.0-r42ha503ecb_0.conda#79f1bd20ee4b918e5885c5f7ed39d086
 https://conda.anaconda.org/conda-forge/linux-64/r-tidygraph-1.2.3-r42ha503ecb_1.conda#feea33bb993df552a5e372312f483394
 https://conda.anaconda.org/conda-forge/noarch/sgkit-0.7.0-pyhd8ed1ab_1.conda#69b4c034ea879749d9e732767649d11a
+https://conda.anaconda.org/bioconda/noarch/qualimap-2.2.2d-hdfd78af_2.tar.bz2#26f6b7758d1584d463603f23019d74fa
 https://conda.anaconda.org/conda-forge/noarch/r-devtools-2.4.5-r42hc72bb7e_2.conda#958eabaabb6477220be4ff8615974fd6
 https://conda.anaconda.org/conda-forge/linux-64/r-ggraph-2.1.0-r42ha503ecb_2.conda#a7eb656842d320749422ecd32bb268f2
 https://conda.anaconda.org/conda-forge/noarch/r-highcharter-0.9.4-r42hc72bb7e_2.conda#2eb82801562f4425b4b8f567c1601681
diff --git a/docs/exercises/variant_filtering/index.qmd b/docs/exercises/variant_filtering/index.qmd
index c395f800..c23e85dc 100644
--- a/docs/exercises/variant_filtering/index.qmd
+++ b/docs/exercises/variant_filtering/index.qmd
@@ -29,7 +29,7 @@ In this exercise we will look at ways of filtering variant data. We
 will begin by applying filters to the variant file containing all
 sites data, followed by a more general approach based on sequencing
 coverage that works also when the variant file lacks information about
-monomorphic sites.
+invariant sites.
 
 ::: {.callout-tip collapse=true}
 
@@ -348,7 +348,6 @@ csvtk summary -t -f MEAN_DEPTH:mean ${OUT}.idepth
 data <- read.table("vcftools/allsites.idepth", header=TRUE)
 LDEPTH_MEAN <- round(mean(data$MEAN_DEPTH), 1)
 ldepth <- sprintf("%.1fX", LDEPTH_MEAN)
-
 ```
 
 Note that `vcftools` treats uncalled sites as missing data, which is
@@ -374,7 +373,10 @@ total depth across all samples.
 
 We plot the distribution of depths by counting how many times each
 depth is observed. This can be done with `csvtk summary` where we
-count positions and group (`-g`) by the `SUM_DEPTH` value:
+count positions and group (`-g`) by the `SUM_DEPTH` value:^[Viewing
+`csvtk` output: either you can **redirect** (`>`) the results from
+`csvtk` to a png output file, or you can **pipe** (`|`) it to the
+command `display`, which should fire up a window with your plot.]
 
 ```{bash }
 #| label: csvtk-plot-vcftools-depth-per-site
diff --git a/docs/slides/foundations/index.qmd b/docs/slides/foundations/index.qmd
index b1847bf1..23a93ab5 100644
--- a/docs/slides/foundations/index.qmd
+++ b/docs/slides/foundations/index.qmd
@@ -18,7 +18,7 @@ format:
 #| echo: false
 #| eval: true
 #| cache: false
-library(viridislite)
+library(viridisLite)
 library(gganimate)
 library(patchwork)
 library(expm)
@@ -444,6 +444,10 @@ The latter expression is called the *nucleotide diversity*
 
 ## Alleles as algebraic entities
 
+:::: {.columns}
+
+::: {.column width="50%"}
+
 Recall: **alleles** refer to *different variants* of a sequence at a
 locus (genomic position).
 
@@ -467,7 +471,11 @@ Will use combination $A$, $a$ for *bi-allelic* loci from now on
 
 :::
 
-::: {.fragment .large}
+:::
+
+::: {.column width="50%"}
+
+::: {.fragment}
 
 ::: {.callout-important appearance="simple" icon=false}
 
@@ -475,24 +483,19 @@ Will use combination $A$, $a$ for *bi-allelic* loci from now on
 
 :::::: {.columns}
 
-::::: {.column width="30%"}
+::::: {.column width="50%"}
 
 [{{< fa solid circle >}}]{style="color: #ff2a2a;"} $A$ red color
 
 {{< fa regular circle >}} $a$ white color
 
-:::::
-
-:::::{.column width="5%"}
-
-:::::
-
-:::::{.column width="20%" .fragment}
+::: {.fragment}
 
 [Punnett square](https://en.wikipedia.org/wiki/Punnett_square)
 
 :::: {style="display: grid; grid-template-columns: auto auto auto;
-grid-row-gap: 0px; grid-column-gap: 0px; text-align: center; align-items: center;"}
+grid-row-gap: 0px; grid-column-gap: 0px; text-align: center;
+align-items: center;"}
 
 :::{}
 
@@ -520,13 +523,13 @@ A
 
 :::{}
 
-![](assets/images/flower-red.svg){width=100}
+![](assets/images/flower-red.svg){width=75}
 
 :::
 
 :::{}
 
-![](assets/images/flower-pink.svg){width=100}
+![](assets/images/flower-pink.svg){width=75}
 
 :::
 
@@ -538,25 +541,27 @@ a
 
 :::{}
 
-![](assets/images/flower-pink.svg){width=100}
+![](assets/images/flower-pink.svg){width=75}
 
 :::
 
 :::{}
 
-![](assets/images/flower-white.svg){width=100}
+![](assets/images/flower-white.svg){width=75}
 
 :::
 
 ::::
 
+:::
+
 :::::
 
 :::::{.column width="5%"}
 
 :::::
 
-::::: {.column width="40%" .fragment}
+::::: {.column width="45%" .fragment}
 
 :::: {style="display: grid; grid-template-columns: 1fr 1fr 1fr 1fr;
 grid-row-gap: 0px; grid-column-gap: 10px; text-align: center; align-items: center;"}
@@ -621,6 +626,10 @@ Heterozygote has intermediate color phenotype (pink).
 
 :::
 
+:::
+
+::::
+
 ::: {.notes}
 
 Until now the examples have been based on nucleotide sequences.
@@ -4218,6 +4227,7 @@ xi <- L / 2
 #| fig-align: center
 #| fig-height: 5
 #| fig-width: 10
+#| fig-format: png
 #| fig-cap: The effect of a selective sweep on
 #|     diversity. The arrow points to the site under selection.
 #|     The y-axis shows Tajima's D which is proportional to the
diff --git a/environment-dev.yml b/environment-dev.yml
index eef28113..4398e6ba 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -1,3 +1,4 @@
+# Development environment
 name: pgip-dev
 channels:
   - conda-forge
@@ -5,12 +6,9 @@ channels:
   - defaults
 dependencies:
   - conda-lock
-  - pip
   - pre-commit
   - r-docopt
-  - r-fontawesome
   - r-languageserver
-  - r-leaflet
   - r-lintr
   - r-precommit
   - pip:
diff --git a/environment-run.yml b/environment-run.yml
deleted file mode 100644
index bcee6062..00000000
--- a/environment-run.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-name: pgip
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bcftools>=1.17
-  - bedtools
-  - csvtk
-  - cyvcf2
-  - d4tools
-  - gatk4
-  - gawk
-  - mosdepth
-  - msprime>=1.2
-  - pip
-  - pyslim
-  - python-newick
-  - samtools
-  - slim>=4.0
-  - tskit>=0.5.0
diff --git a/environment-site.yml b/environment-site.yml
deleted file mode 100644
index d0d82155..00000000
--- a/environment-site.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-name: pgip
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - ca-certificates
-  - demesdraw
-  - jupyter
-  - jupyter-cache
-  - python=3.10
-  - r-codetools
-  - r-rmarkdown>=2.19
diff --git a/environment.yml b/environment.yml
index 55678327..d2483d33 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,6 +9,7 @@ dependencies:
   - bedtools
   - bcftools
   - bokeh
+  - bwa
   - ca-certificates
   - csvtk
   - cyvcf2=0.30.16
@@ -25,10 +26,11 @@ dependencies:
   - multiqc
   - pandas
   - pip
+  - picard
   - pyslim
   - python>=3.10
   - python-newick
-  # - r-animation
+  - qualimap
   - r-ape
   - r-codetools
   - r-curl
@@ -48,8 +50,6 @@ dependencies:
   - r-gsalib
   - r-highcharter
   - r-igraph
-  # # - r-irkernel
-  # # - r-jsonlite
   - r-kableextra
   - r-latex2exp
   - r-leaflet
@@ -58,20 +58,16 @@ dependencies:
   - r-patchwork
   - r-pdftools
   - r-plotly
-  # # - r-reactable
   - r-readr
   - r-readxl
   - r-reticulate
   - r-rmarkdown>=2.19
   - r-tidyr
-  # # - r-transformr
   - r-viridis
   - samtools=1.15.1
-  # # - scikit-learn
   - scikit-allel
   - slim>=4.0
   - sgkit
   - tskit>=0.5.0
+  - vcflib
   - vcftools
-  # # - tqdm
-  # # - yarl
diff --git a/requirements-dev.txt b/requirements-dev.txt
deleted file mode 100644
index de89e5ad..00000000
--- a/requirements-dev.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-click
-conda-lock
-joblib
-pre_commit
-tqdm
-editorconfig-checker
diff --git a/requirements-dev.yml b/requirements-dev.yml
deleted file mode 100644
index 45f1060e..00000000
--- a/requirements-dev.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - r-animation
-  - r-codetools
-  - r-dotenv
-  - r-gganimate
-  - r-ggplot2
-  - r-gifski
-  - r-igraph
-  - r-irkernel
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index fb9b47f3..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-bokeh
-cyvcf2
-demes
-demesdraw
-jupyter
-matplotlib>=3.4.0
-msprime>=1.0
-networkx
-newick
-numpy
-scikit-allel
-sgkit
-sphinx
-tqdm
-tskit>=0.5
diff --git a/scripts/condalock.sh b/scripts/condalock.sh
index e4e2f3b7..1b1279e5 100755
--- a/scripts/condalock.sh
+++ b/scripts/condalock.sh
@@ -4,7 +4,7 @@ set -xeuo pipefail
 if [[ $# == 1 ]]; then
     if [[ "$1" == "--force" ]]; then
         echo "generating conda-linux-64.lock from environment.yml"
-        conda-lock --kind explicit --platform linux-64
+        conda-lock lock -f environment.yml --kind explicit --platform linux-64
     else
         echo "Usage: $0 [--force]"
         exit 1