diff --git a/.bumpversion.toml b/.bumpversion.toml
index 8742b07c..039b57af 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "2.3.1"
+current_version = "2.3.1.9001"
 search = "{current_version}"
 replace = "{new_version}"
 message = "Bump version: {current_version} → {new_version}"
diff --git a/.github/workflows/build_conda_recipes.yaml b/.github/workflows/build_conda_recipes.yaml
index efe342df..b576f803 100644
--- a/.github/workflows/build_conda_recipes.yaml
+++ b/.github/workflows/build_conda_recipes.yaml
@@ -12,7 +12,7 @@ env:
   conda_env_yaml: conda/env/yaml
   conda_env_lock: conda/env/lock
   conda_org: pcgr
-  VERSION: '2.3.1' # bump
+  VERSION: '2.3.1.9001' # bump
 jobs:
   conda_build:
     # When merging to one of the branches above and the commit message matches
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index 7312d72f..37d85cd0 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-sigven@ifi.uio.no.
+sigven@ifi.uio.no or peterdiakumis@gmail.com.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 00000000..88a69f93
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,133 @@
+# Contributing to PCGR
+
+Thanks for your interest in contributing to the Personal Cancer Genome Reporter
+(PCGR). Contributions of all kinds are welcome — bug reports, documentation
+improvements, feature suggestions, and code.
+
+This document explains how to report problems and how to propose changes.
+
+## Code of conduct
+
+This project follows a [Code of Conduct](CODE_OF_CONDUCT.md). By participating,
+you are expected to uphold it. Please report unacceptable behaviour to the
+maintainers.
+
+## Ways to contribute
+
+- **Report a bug** — open an issue (see below for what to include)
+- **Request a feature** — open an issue describing the use case
+- **Ask a question** — use GitHub Discussions or open an issue
+- **Improve documentation** — corrections and clarifications are very welcome
+- **Contribute code** — see *Development workflow* below
+
+## Reporting bugs
+
+Most issues we receive can only be diagnosed with the full run context, so
+please include **all** of the following. Issues without this information will
+usually need a follow-up before we can help.
+
+1. **PCGR version** (`pcgr --version`)
+2. **Reference data bundle version** and the genome assembly used
+   (`grch37` or `grch38`)
+3. **Installation method** — Conda, Docker, Singularity/Apptainer —
+   including the image tag or environment specification
+4. **Operating system** and, if relevant, the compute environment
+   (laptop, HPC/cluster, cloud)
+5. **The exact command you ran**, in full, with all arguments
+6. **The complete error message and log output** (please paste as text in a
+   fenced code block rather than as a screenshot)
+7. **Input characteristics** — variant caller used, approximate number of
+   variants, tumour type, whether CNA/expression/fusion input was supplied
+8. **A minimal example input** that reproduces the problem, if you are able to
+   share one
+
+Please do not attach patient-identifiable data to a public issue. If a problem
+can only be reproduced with sensitive data, say so in the issue and we will
+find another way to investigate.
+
+## Requesting features
+
+When proposing a feature, describe the scientific or clinical use case rather
+than only the implementation. PCGR aims to produce clinically interpretable
+output aligned with established guidelines (AMP/ASCO/CAP, ClinGen/CGC/VICC), so
+proposals that affect variant classification or tier assignment should reference
+the relevant guideline or evidence source.
+
+## Development workflow
+
+We use a simple two-branch model:
+
+- **`main`** — reflects the current released version. Do not open pull requests
+  against `main`.
+- **`dev`** — the active development branch. **All pull requests should target
+  `dev`.**
+
+To contribute code:
+
+1. Fork the repository and create a branch from `dev`
+   (e.g. `feature/short-description` or `fix/short-description`)
+2. Make your changes, keeping the pull request focused on a single concern
+3. Update documentation and the changelog where relevant
+4. Open a pull request against `dev`, describing **what** the change does and
+   **why** it is needed
+
+For anything substantial — new annotation sources, changes to classification or
+tiering logic, or architectural changes — please open an issue to discuss the
+approach before writing code. This saves time on both sides.
+
+## Code organisation
+
+PCGR spans two languages, and it helps to know where a change belongs:
+
+- **Python** — the pipeline, variant annotation, and much of the interpretation
+  logic (including oncogenicity classification and biomarker matching)
+- **R** (the [`pcgrr`](https://github.com/sigven/pcgrr) package) — report
+  generation and visualisation via Quarto, together with parts of the clinical
+  interpretation logic, notably AMP/ASCO/CAP tier assignment
+
+Note that this split is not absolute: some classification logic currently lives
+in `pcgrr` alongside the reporting code. If you are unsure where a change
+belongs, open an issue and ask before starting work.
+
+## Coding conventions
+
+- Follow the style of the surrounding code
+- Python: follow PEP 8 where practical; add docstrings to new functions
+- R: follow the existing style in `pcgrr`
+- Keep commits reasonably self-contained with descriptive messages
+- Do **not** commit reference data bundles, large binary files, or test data
+  containing patient information
+
+## Testing and validation
+
+Automated test coverage is currently limited and is actively being expanded. In
+the meantime, we ask contributors to describe how a change was validated:
+
+- State the command(s) you ran to exercise the change
+- For changes affecting annotation, classification or tiering, show the effect
+  on output — for example, the relevant rows or fields before and after
+- Confirm that an end-to-end run completes on example data
+- Where tests exist, please run them and add new ones covering your change
+
+Continuous integration runs automatically on pull requests. Please make sure it
+passes before requesting review.
+
+## Releases and versioning
+
+PCGR follows semantic versioning. Releases are cut from `dev` into `main` by the
+maintainers, accompanied by an updated changelog. Reference data bundles are
+versioned separately and tied to specific releases — see the documentation for
+the compatible bundle for each version.
+
+## Licence
+
+PCGR is released under the MIT licence. By contributing, you agree that your
+contributions will be licensed under the same terms.
+
+## Getting in touch
+
+- **Bugs and feature requests** — GitHub Issues
+- **Questions and general discussion** — GitHub Discussions (to come)
+- **Documentation** — https://sigven.github.io/pcgr/
+
+Thanks for your effort to improve PCGR!
diff --git a/README.md b/README.md
index e224952e..1d08eb26 100755
--- a/README.md
+++ b/README.md
@@ -153,6 +153,15 @@ Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Mykleb
 
 Sigve Nakken, Vladislav Saveliev, Oliver Hofmann, Pål Møller, Ola Myklebost, and Eivind Hovig. **Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer** (2021). *Int J Cancer*. [doi:[10.1002/ijc.33749](doi:%5B10.1002/ijc.33749)](https://doi.org/10.1002/ijc.33749)
 
+## Contributing
+
+Contributions are welcome — bug reports, documentation improvements, feature
+suggestions, and code. See [CONTRIBUTING.md](CONTRIBUTING.md) for how to report
+issues and submit pull requests (note that all PRs should target the `dev`
+branch).
+
+This project follows a [Code of Conduct](CODE_OF_CONDUCT.md).
+
 ## Contact
 
 sigven AT ifi.uio.no
diff --git a/conda/env/lock/pcgr-linux-64.lock b/conda/env/lock/pcgr-linux-64.lock
index 21069b70..d8f4ade5 100644
--- a/conda/env/lock/pcgr-linux-64.lock
+++ b/conda/env/lock/pcgr-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 1ec58a3c43c9bc30f5f3b852b906989ca340384dd3031d2650e4fdb4f8e3bf41
+# input_hash: 868c4c18f3fadbaa7bd7a61f045f2b530f3721bcdad9ba4ba30c6c41ca08f354
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda#86d9cba083cd041bfbf242a01a7a1999
 https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-openmpi.tar.bz2#1dcc49e16749ff79ba2194fa5d4ca5e7
@@ -71,7 +71,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.cond
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda#27329162c0dc732bcf67a4e0cd488125
 https://conda.anaconda.org/bioconda/linux-64/muscle-3.8.1551-h9948957_9.tar.bz2#abeab9c9f2802eae4f867260650837f6
 https://conda.anaconda.org/bioconda/linux-64/mustang-3.2.4-h9948957_0.tar.bz2#20af4690d0bcf66aaf5dd81056557b2d
-https://conda.anaconda.org/conda-forge/linux-64/p11-kit-0.26.2-h3435931_0.conda#312989f1b7318c3763fffdc78df8474e
+https://conda.anaconda.org/conda-forge/linux-64/p11-kit-0.26.4-h3435931_0.conda#9980feddc5ad41bac53f7396376e6a2f
 https://conda.anaconda.org/bioconda/linux-64/prank-170427-h9948957_1.tar.bz2#b42e651a06117c624a977b6a24b1006d
 https://conda.anaconda.org/bioconda/linux-64/proda-1.0-h503566f_7.tar.bz2#056c35aac8bf387652e54e5553a2ddf4
 https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
@@ -179,7 +179,7 @@ https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.9-pyhd8ed1a
 https://conda.anaconda.org/conda-forge/noarch/click-8.4.2-pyhc90fa1f_0.conda#2c4bd6aeb90bb157456841c3270a0d92
 https://conda.anaconda.org/bioconda/noarch/dendropy-5.0.8-pyhdfd78af_1.tar.bz2#0fa94922431d1074792639704d19461d
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
-https://conda.anaconda.org/conda-forge/linux-64/gawk-5.4.0-h0a3468a_0.conda#85817e8a5230ebde83b9ca2a8282e004
+https://conda.anaconda.org/conda-forge/linux-64/gawk-5.4.1-h0a3468a_0.conda#64fd8d804a6aaef55d6d6c562446d72b
 https://conda.anaconda.org/conda-forge/linux-64/gnutls-3.8.13-h18acefa_0.conda#7c3de21891993e89aabdadaa603ed835
 https://conda.anaconda.org/conda-forge/noarch/hpack-4.2.0-pyhd8ed1ab_0.conda#b395909221b9bd1df066e5930e18855b
 https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h5efdd21_0.tar.bz2#06b995dc2244c024b45bbb3e53ae2f27
@@ -300,7 +300,7 @@ https://conda.anaconda.org/bioconda/noarch/perl-www-robotrules-6.03-pl5321hdfd78
 https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda#4a85203c1d80c1059086ae860836ffb9
 https://conda.anaconda.org/bioconda/linux-64/t-coffee-13.46.2.7c9e712d-pl5321hb2a3317_0.conda#079c99f8f1e607b7ffb8e987ff1658b2
 https://conda.anaconda.org/pcgr/noarch/oncokb-annotator-3.4.1.9000-py_0.conda#4f4a8e7191568018f74eccd095a92fa5
-https://conda.anaconda.org/pcgr/noarch/pcgr-2.3.1-pyh4616a5c_0.conda#fe999077681478b304a7aa953d9db3cb
+https://conda.anaconda.org/pcgr/label/dev/noarch/pcgr-2.3.1.9001-pyh4616a5c_0.conda#be2389dcb4d06fbfaf341fe06ef6fbf4
 https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5321hdfd78af_5.tar.bz2#932416c9ba6a9af43609e04ec5952574
 https://conda.anaconda.org/bioconda/noarch/perl-extutils-parsexs-3.63-pl5321hdfd78af_0.conda#1226e6d34340cfe6a3a17c0bc80677e4
 https://conda.anaconda.org/bioconda/linux-64/perl-html-parser-3.81-pl5321h4ac6f70_1.tar.bz2#6ef96e2df04cabd48c4c888c1ec57523
diff --git a/conda/env/lock/pcgr-osx-64.lock b/conda/env/lock/pcgr-osx-64.lock
index 391d12d1..1ff8590c 100644
--- a/conda/env/lock/pcgr-osx-64.lock
+++ b/conda/env/lock/pcgr-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 7b534fc8e245f0b241e31d303fa12120590f0328c3e2f6b4649f66ebe9735111
+# input_hash: 94e6ce1a0b64e53fc39edca15197e4439d6583440c20235917af93cf502ea6e6
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/osx-64/argtable2-2.13-h10d778d_1004.conda#7ebcbc431363dfbf9ae25e6a7205d414
 https://conda.anaconda.org/bioconda/osx-64/consan-1.2-h18d8cf3_7.tar.bz2#219f6fde78a3bc5218a03b8a58403982
@@ -102,7 +102,7 @@ https://conda.anaconda.org/bioconda/osx-64/muscle-3.8.1551-h5fa12a8_9.tar.bz2#5c
 https://conda.anaconda.org/bioconda/osx-64/mustang-3.2.4-h5fa12a8_0.tar.bz2#a8ffe82e58268ed224ceffefade2bd7a
 https://conda.anaconda.org/conda-forge/osx-64/openjdk-22.0.1-h2d185b6_0.conda#46e7a579254f336dd53b8d7ab211b347
 https://conda.anaconda.org/conda-forge/osx-64/openssl-3.6.3-hc881268_0.conda#46be42ab403712fd349d007d763bf767
-https://conda.anaconda.org/conda-forge/osx-64/p11-kit-0.26.2-hd1f9c09_0.conda#abbc95fa774bb9816321aa784f1ca4be
+https://conda.anaconda.org/conda-forge/osx-64/p11-kit-0.26.4-h8c408c4_0.conda#23ccceae47c2e20d756fd689ce691ea5
 https://conda.anaconda.org/conda-forge/osx-64/pcre-8.45-he49afe7_0.tar.bz2#0526850419e04ac003bc0b65a78dc4cc
 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7
 https://conda.anaconda.org/conda-forge/osx-64/perl-clone-0.46-pl5321h6e16a3a_1.conda#626270fdfe8fa1cf8b2edfc14a9524a4
@@ -167,7 +167,7 @@ https://conda.anaconda.org/bioconda/osx-64/probcons-1.12-hd174df1_1.tar.bz2#bdf9
 https://conda.anaconda.org/conda-forge/osx-64/xz-5.8.3-h6a5a847_0.conda#65aa14eb080715ecf13b15e5d85acde2
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 https://conda.anaconda.org/conda-forge/osx-64/cyrus-sasl-2.1.28-h610c526_0.conda#314cd5e4aefc50fec5ffd80621cfb4f8
-https://conda.anaconda.org/conda-forge/osx-64/gawk-5.4.0-h37db40e_0.conda#d2d12e7acdc045ac5938eca2c1506c4a
+https://conda.anaconda.org/conda-forge/osx-64/gawk-5.4.1-h37db40e_0.conda#3154d75effe472881632e2cf871b4ddc
 https://conda.anaconda.org/conda-forge/osx-64/gnutls-3.8.13-hba17655_0.conda#3bd287df19905ac759f8854ccafb388f
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@@ -284,7 +284,7 @@ https://conda.anaconda.org/bioconda/osx-64/pybedtools-0.10.0-py312ha99f805_2.tar
 https://conda.anaconda.org/conda-forge/osx-64/scipy-1.18.0-py312h6309490_0.conda#7c6973eecefc02ccdbaa35fca709ff71
 https://conda.anaconda.org/conda-forge/osx-64/compiler-rt-18.1.7-h734a56e_0.conda#249c794de0d8eb83f7a4d6e4affdbe34
 https://conda.anaconda.org/bioconda/osx-64/pasta-1.9.2-py312h7e1f36d_5.tar.bz2#2253ed9b2abeb41417ed72117ccd2d9d
-https://conda.anaconda.org/pcgr/noarch/pcgr-2.3.1-pyh4616a5c_0.conda#fe999077681478b304a7aa953d9db3cb
+https://conda.anaconda.org/pcgr/label/dev/noarch/pcgr-2.3.1.9001-pyh4616a5c_0.conda#be2389dcb4d06fbfaf341fe06ef6fbf4
 https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5321hdfd78af_4.tar.bz2#1b4b260b45e9cac33fcb45918cda428b
 https://conda.anaconda.org/bioconda/noarch/vcf2maf-1.6.22-hdfd78af_2.conda#5f3dd4ce7d622798e5c38d6099a02c7c
 https://conda.anaconda.org/bioconda/noarch/vcf2tsvpy-0.6.2-pyhb241bb5_0.conda#a79af1a6bffe5de2bc55ad56329da38c
diff --git a/conda/env/lock/pcgrr-linux-64.lock b/conda/env/lock/pcgrr-linux-64.lock
index d5f1e72d..866a717b 100644
--- a/conda/env/lock/pcgrr-linux-64.lock
+++ b/conda/env/lock/pcgrr-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: b832532dbfc9b8ca2b3bb04061da7a2fb3e73ac939312c4b99140c29aa8f6e68
+# input_hash: 907f055d21fdb356b803a834f75fadf30f6ca1703082e8e112784436fcaeeddc
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
 https://conda.anaconda.org/conda-forge/linux-64/dart-sass-1.101.0-hfc2019e_0.conda#3c5956f8de352968510d857a1dfdf929
@@ -37,7 +37,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a3
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 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88
-https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.4.1-hb03c661_0.conda#6178c6f2fb254558238ef4e6c56fb782
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.2.0-hb03c661_0.conda#466badda5536d85ddc63ee9404f29735
 https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb
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@@ -331,5 +331,5 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.h
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.5-r45hdfd78af_4.conda#4baa0dd494a2955755bb00fcd0242f00
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-https://conda.anaconda.org/pcgr/noarch/r-pcgrr-2.3.1-h4616a5c_0.conda#15cb05daf8edd1b6b488651bd553dd1a
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-2.3.0-h4616a5c_0.conda#00834de27a1f7e2a41953f72b48dfcdb
+https://conda.anaconda.org/pcgr/label/dev/noarch/r-pcgrr-2.3.1.9001-h4616a5c_0.conda#b44c3c14e2af1087ad753de83a2a2601
+https://conda.anaconda.org/pcgr/label/dev/noarch/r-cpsr-2.2.5.9012-h4616a5c_0.conda#28080c1c508222229783123de6b5e4e7
diff --git a/conda/env/lock/pcgrr-osx-64.lock b/conda/env/lock/pcgrr-osx-64.lock
index d89c6d44..3ae69dc8 100644
--- a/conda/env/lock/pcgrr-osx-64.lock
+++ b/conda/env/lock/pcgrr-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: db8905790bb8ad9f4c8e5fb6cfd86de4c4c86790afc1fa3a1fba4ebb34f4e2c0
+# input_hash: c47ae735e100df730b668ef9667c287d56fa7fe34db0d361446df94e4880a6a7
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
 https://conda.anaconda.org/conda-forge/noarch/compiler-rt22_osx-64-22.1.8-hcf80936_1.conda#bcf37da1bdd75d1a3c313e3c06561357
@@ -31,7 +31,7 @@ https://conda.anaconda.org/conda-forge/osx-64/libexpat-2.8.1-hcc62823_1.conda#dc
 https://conda.anaconda.org/conda-forge/osx-64/libffi-3.5.2-hd1f9c09_0.conda#66a0dc7464927d0853b590b6f53ba3ea
 https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_osx-64-15.2.0-h49bd711_119.conda#3dc239fadd30c8534716d80346c5ba6d
 https://conda.anaconda.org/conda-forge/osx-64/libiconv-1.18-h57a12c2_2.conda#210a85a1119f97ea7887188d176db135
-https://conda.anaconda.org/conda-forge/osx-64/libjpeg-turbo-3.1.4.1-ha1e9b39_0.conda#57cc1464d457d01ac78f5860b9ca1714
+https://conda.anaconda.org/conda-forge/osx-64/libjpeg-turbo-3.2.0-ha1e9b39_0.conda#d86c1b9259377fb4dcd76fe7472bd2d2
 https://conda.anaconda.org/conda-forge/osx-64/liblzma-5.8.3-hbb4bfdb_0.conda#becdfbfe7049fa248e52aa37a9df09e2
 https://conda.anaconda.org/conda-forge/osx-64/libmpdec-4.0.0-hf3981d6_1.conda#ec88ba8a245855935b871a7324373105
 https://conda.anaconda.org/conda-forge/osx-64/libuv-1.52.1-ha3d0635_0.conda#703303067839cd1da659528a84b3c0cc
@@ -338,5 +338,5 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.h
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.5-r45hdfd78af_4.conda#4baa0dd494a2955755bb00fcd0242f00
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-variantannotation-1.56.0-r45h010771c_0.conda#2bc0fa9167469b8ee04400d3b7d3e7f3
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.19.1-r45hdfd78af_0.conda#8a1832a474ae43bb4b015b5a106dbe04
-https://conda.anaconda.org/pcgr/noarch/r-pcgrr-2.3.1-h4616a5c_0.conda#15cb05daf8edd1b6b488651bd553dd1a
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-2.3.0-h4616a5c_0.conda#00834de27a1f7e2a41953f72b48dfcdb
+https://conda.anaconda.org/pcgr/label/dev/noarch/r-pcgrr-2.3.1.9001-h4616a5c_0.conda#b44c3c14e2af1087ad753de83a2a2601
+https://conda.anaconda.org/pcgr/label/dev/noarch/r-cpsr-2.2.5.9012-h4616a5c_0.conda#28080c1c508222229783123de6b5e4e7
diff --git a/conda/env/yaml/pcgr.yaml b/conda/env/yaml/pcgr.yaml
index 68a5516e..21c2568b 100644
--- a/conda/env/yaml/pcgr.yaml
+++ b/conda/env/yaml/pcgr.yaml
@@ -6,7 +6,7 @@ channels:
   - bioconda
 
 dependencies:
-  - pcgr ==2.3.1 # bump
+  - pcgr ==2.3.1.9001 # bump
   - bioconda::bedtools
   - bioconda::bcftools
   - bioconda::ensembl-vep ==115.1
diff --git a/conda/env/yaml/pcgrr.yaml b/conda/env/yaml/pcgrr.yaml
index 9209e3ed..839b97f5 100644
--- a/conda/env/yaml/pcgrr.yaml
+++ b/conda/env/yaml/pcgrr.yaml
@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - r-pcgrr ==2.3.1 # bump
+  - r-pcgrr ==2.3.1.9001 # bump
   - r-cpsr
   - r-argparse
   - bioconductor-bsgenome.hsapiens.ucsc.hg38
diff --git a/conda/env/yaml/pkgdown.yaml b/conda/env/yaml/pkgdown.yaml
index 0c069835..f8dd76ea 100644
--- a/conda/env/yaml/pkgdown.yaml
+++ b/conda/env/yaml/pkgdown.yaml
@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - r-pcgrr ==2.3.1 # bump
+  - r-pcgrr ==2.3.1.9001 # bump
   - r-pkgdown
   - r-readr
   - r-glue
diff --git a/conda/recipe/pcgr/recipe.yaml b/conda/recipe/pcgr/recipe.yaml
index dbafd17e..a15260ab 100644
--- a/conda/recipe/pcgr/recipe.yaml
+++ b/conda/recipe/pcgr/recipe.yaml
@@ -1,6 +1,6 @@
 context:
   name: pcgr
-  version: 2.3.1 # bump
+  version: 2.3.1.9001 # bump
 
 package:
   name: ${{ name|lower }}
diff --git a/conda/recipe/pcgrr/recipe.yaml b/conda/recipe/pcgrr/recipe.yaml
index 55d8c538..5302ea22 100644
--- a/conda/recipe/pcgrr/recipe.yaml
+++ b/conda/recipe/pcgrr/recipe.yaml
@@ -1,6 +1,6 @@
 context:
   name: r-pcgrr
-  version: 2.3.1 # bump
+  version: 2.3.1.9001 # bump
 
 package:
   name: ${{ name|lower }}
diff --git a/pcgr/_version.py b/pcgr/_version.py
index 3fb09e53..60e25a63 100644
--- a/pcgr/_version.py
+++ b/pcgr/_version.py
@@ -1 +1 @@
-__version__ = '2.3.1' # bump
+__version__ = '2.3.1.9001' # bump
diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION
index c3e5e74c..67cb2c13 100644
--- a/pcgrr/DESCRIPTION
+++ b/pcgrr/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pcgrr
 Type: Package
 Title: Personal Cancer Genome ReporteR
-Version: 2.3.1
+Version: 2.3.1.9001
 Authors@R:
     c(person(given = "Sigve",
              family = "Nakken",
diff --git a/pcgrr/R/oncokb.R b/pcgrr/R/oncokb.R
index 50ea3e75..f7aa22f7 100644
--- a/pcgrr/R/oncokb.R
+++ b/pcgrr/R/oncokb.R
@@ -1130,8 +1130,25 @@ process_oncokb_maf <-
 
     # Process HGVSp file (protein changes)
     if (!is.null(maf_file_hgvsp) && file.exists(maf_file_hgvsp)) {
+      # Force character typing for all columns (except the known boolean
+      # flag columns) rather than relying on readr's per-file column type
+      # guessing: the HGVSp and HGVSg MAF files are read independently, so
+      # a sparsely populated pass-through column (e.g.
+      # MUTATION_EFFECT_CITATIONS) can be guessed as a different type
+      # (character/double/logical) in each file, which later breaks
+      # dplyr::bind_rows() when rows from both files are combined into
+      # all_variant_annotations. ANNOTATED/GENE_IN_ONCOKB/VARIANT_IN_ONCOKB
+      # are kept as logical since they're compared with `== TRUE` below;
+      # forcing them to character would make that filter match nothing
+      # (OncoKB's MafAnnotator writes Python-style "True"/"False", and
+      # "True" == TRUE is FALSE in R, not a match).
       maf_hgvsp <- readr::read_tsv(
-        maf_file_hgvsp, show_col_types = FALSE)
+        maf_file_hgvsp, show_col_types = FALSE,
+        col_types = readr::cols(
+          ANNOTATED = readr::col_logical(),
+          GENE_IN_ONCOKB = readr::col_logical(),
+          VARIANT_IN_ONCOKB = readr::col_logical(),
+          .default = readr::col_character()))
 
       # Filter for variants in OncoKB genes regardless of ANNOTATED flag:
       # the MAF annotator batch endpoint misses variants covered only by gene-level
@@ -1277,8 +1294,18 @@ process_oncokb_maf <-
 
     # Process HGVSg file (considering non-protein changes)
     if (!is.null(maf_file_hgvsg) && file.exists(maf_file_hgvsg)) {
+      # Same rationale as the HGVSp read above: force character typing so
+      # this file's per-column type guesses can't diverge from the HGVSp
+      # file's and break the later dplyr::bind_rows() of both, while
+      # keeping the boolean flag columns logical so `== TRUE` filters
+      # below still work.
       maf_hgvsg <- readr::read_tsv(
-        maf_file_hgvsg, show_col_types = FALSE)
+        maf_file_hgvsg, show_col_types = FALSE,
+        col_types = readr::cols(
+          ANNOTATED = readr::col_logical(),
+          GENE_IN_ONCOKB = readr::col_logical(),
+          VARIANT_IN_ONCOKB = readr::col_logical(),
+          .default = readr::col_character()))
 
       # Filter for variants in OncoKB genes without a protein change (HGVSg path),
       # regardless of ANNOTATED flag — same reasoning as HGVSp path above
diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd
index 4c9d43d9..49b07ed6 100644
--- a/pcgrr/vignettes/installation.Rmd
+++ b/pcgrr/vignettes/installation.Rmd
@@ -15,7 +15,7 @@ require(glue, include.only = "glue")
 
 ```{r vars, echo=FALSE}
 Sys.setenv(VEP_VERSION = "115")
-Sys.setenv(PCGR_VERSION = "2.3.1")
+Sys.setenv(PCGR_VERSION = "2.3.1.9001")
 Sys.setenv(BUNDLE_VERSION = "20260620")
 VEP_VERSION <- Sys.getenv("VEP_VERSION")
 PCGR_VERSION <- Sys.getenv("PCGR_VERSION")
diff --git a/pyproject.toml b/pyproject.toml
index 04a23d1d..1029c1d3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pcgr"
-version = "2.3.1" # bump
+version = "2.3.1.9001" # bump
 description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine"
 authors = [
     {name = "Sigve Nakken", email = "sigven@gmail.com"},