vartrace 0.1.0__tar.gz

vartrace-0.1.0/.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

vartrace-0.1.0/.gitignore

@@ -0,0 +1,25 @@
+# pixi
+.pixi/*
+!.pixi/config.toml
+
+# Python
+__pycache__/
+*.py[cod]
+.pytest_cache/
+*.egg-info/
+build/
+dist/
+
+# геномни данни никога не влизат в хранилището
+*.vcf
+*.vcf.gz
+*.bam
+*.bai
+*.cram
+*.fastq
+*.fastq.gz
+*.fq.gz
+data/
+
+# macOS
+.DS_Store

vartrace-0.1.0/LICENSE

@@ -0,0 +1,75 @@
+Required Notice: Copyright (c) 2026 Kamen Yovchev
+
+# PolyForm Noncommercial License 1.0.0
+
+<https://polyformproject.org/licenses/noncommercial/1.0.0>
+
+## Acceptance
+
+In order to get any license under these terms, you must agree to them as both strict obligations and conditions to all your licenses.
+
+## Copyright License
+
+The licensor grants you a copyright license for the software to do everything you might do with the software that would otherwise infringe the licensor's copyright in it for any permitted purpose.  However, you may only distribute the software according to [Distribution License](#distribution-license) and make changes or new works based on the software according to [Changes and New Works License](#changes-and-new-works-license).
+
+## Distribution License
+
+The licensor grants you an additional copyright license to distribute copies of the software.  Your license to distribute covers distributing the software with changes and new works permitted by [Changes and New Works License](#changes-and-new-works-license).
+
+## Notices
+
+You must ensure that anyone who gets a copy of any part of the software from you also gets a copy of these terms or the URL for them above, as well as copies of any plain-text lines beginning with `Required Notice:` that the licensor provided with the software.  For example:
+
+> Required Notice: Copyright Yoyodyne, Inc. (http://example.com)
+
+## Changes and New Works License
+
+The licensor grants you an additional copyright license to make changes and new works based on the software for any permitted purpose.
+
+## Patent License
+
+The licensor grants you a patent license for the software that covers patent claims the licensor can license, or becomes able to license, that you would infringe by using the software.
+
+## Noncommercial Purposes
+
+Any noncommercial purpose is a permitted purpose.
+
+## Personal Uses
+
+Personal use for research, experiment, and testing for the benefit of public knowledge, personal study, private entertainment, hobby projects, amateur pursuits, or religious observance, without any anticipated commercial application, is use for a permitted purpose.
+
+## Noncommercial Organizations
+
+Use by any charitable organization, educational institution, public research organization, public safety or health organization, environmental protection organization, or government institution is use for a permitted purpose regardless of the source of funding or obligations resulting from the funding.
+
+## Fair Use
+
+You may have "fair use" rights for the software under the law. These terms do not limit them.
+
+## No Other Rights
+
+These terms do not allow you to sublicense or transfer any of your licenses to anyone else, or prevent the licensor from granting licenses to anyone else.  These terms do not imply any other licenses.
+
+## Patent Defense
+
+If you make any written claim that the software infringes or contributes to infringement of any patent, your patent license for the software granted under these terms ends immediately. If your company makes such a claim, your patent license ends immediately for work on behalf of your company.
+
+## Violations
+
+The first time you are notified in writing that you have violated any of these terms, or done anything with the software not covered by your licenses, your licenses can nonetheless continue if you come into full compliance with these terms, and take practical steps to correct past violations, within 32 days of receiving notice.  Otherwise, all your licenses end immediately.
+
+## No Liability
+
+***As far as the law allows, the software comes as is, without any warranty or condition, and the licensor will not be liable to you for any damages arising out of these terms or the use or nature of the software, under any kind of legal claim.***
+
+## Definitions
+
+The **licensor** is the individual or entity offering these terms, and the **software** is the software the licensor makes available under these terms.
+
+**You** refers to the individual or entity agreeing to these terms.
+
+**Your company** is any legal entity, sole proprietorship, or other kind of organization that you work for, plus all organizations that have control over, are under the control of, or are under common control with that organization.  **Control** means ownership of substantially all the assets of an entity, or the power to direct its management and policies by vote, contract, or otherwise.  Control can be direct or indirect.
+
+**Your licenses** are all the licenses granted to you for the software under these terms.
+
+**Use** means anything you do with the software requiring one of your licenses.

vartrace-0.1.0/LICENSE-MODELS

@@ -0,0 +1,413 @@
+The trained models in vartrace/models/ are licensed under the Creative Commons
+Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).
+
+Copyright (c) 2026 Kamen Yovchev
+
+Attribution-NonCommercial 4.0 International
+
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
+does not provide legal services or legal advice. Distribution of
+Creative Commons public licenses does not create a lawyer-client or
+other relationship. Creative Commons makes its licenses and related
+information available on an "as-is" basis. Creative Commons gives no
+warranties regarding its licenses, any material licensed under their
+terms and conditions, or any related information. Creative Commons
+disclaims all liability for damages resulting from their use to the
+fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and
+conditions that creators and other rights holders may use to share
+original works of authorship and other material subject to copyright
+and certain other rights specified in the public license below. The
+following considerations are for informational purposes only, are not
+exhaustive, and do not form part of our licenses.
+
+     Considerations for licensors: Our public licenses are
+     intended for use by those authorized to give the public
+     permission to use material in ways otherwise restricted by
+     copyright and certain other rights. Our licenses are
+     irrevocable. Licensors should read and understand the terms
+     and conditions of the license they choose before applying it.
+     Licensors should also secure all rights necessary before
+     applying our licenses so that the public can reuse the
+     material as expected. Licensors should clearly mark any
+     material not subject to the license. This includes other CC-
+     licensed material, or material used under an exception or
+     limitation to copyright. More considerations for licensors:
+    wiki.creativecommons.org/Considerations_for_licensors
+
+     Considerations for the public: By using one of our public
+     licenses, a licensor grants the public permission to use the
+     licensed material under specified terms and conditions. If
+     the licensor's permission is not necessary for any reason--for
+     example, because of any applicable exception or limitation to
+     copyright--then that use is not regulated by the license. Our
+     licenses grant only permissions under copyright and certain
+     other rights that a licensor has authority to grant. Use of
+     the licensed material may still be restricted for other
+     reasons, including because others have copyright or other
+     rights in the material. A licensor may make special requests,
+     such as asking that all changes be marked or described.
+     Although not required by our licenses, you are encouraged to
+     respect those requests where reasonable. More considerations
+     for the public:
+    wiki.creativecommons.org/Considerations_for_licensees
+
+=======================================================================
+
+Creative Commons Attribution-NonCommercial 4.0 International Public
+License
+
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution-NonCommercial 4.0 International Public License ("Public
+License"). To the extent this Public License may be interpreted as a
+contract, You are granted the Licensed Rights in consideration of Your
+acceptance of these terms and conditions, and the Licensor grants You
+such rights in consideration of benefits the Licensor receives from
+making the Licensed Material available under these terms and
+conditions.
+
+
+Section 1 -- Definitions.
+
+  a. Adapted Material means material subject to Copyright and Similar
+     Rights that is derived from or based upon the Licensed Material
+     and in which the Licensed Material is translated, altered,
+     arranged, transformed, or otherwise modified in a manner requiring
+     permission under the Copyright and Similar Rights held by the
+     Licensor. For purposes of this Public License, where the Licensed
+     Material is a musical work, performance, or sound recording,
+     Adapted Material is always produced where the Licensed Material is
+     synched in timed relation with a moving image.
+
+  b. Adapter's License means the license You apply to Your Copyright
+     and Similar Rights in Your contributions to Adapted Material in
+     accordance with the terms and conditions of this Public License.
+
+  c. Copyright and Similar Rights means copyright and/or similar rights
+     closely related to copyright including, without limitation,
+     performance, broadcast, sound recording, and Sui Generis Database
+     Rights, without regard to how the rights are labeled or
+     categorized. For purposes of this Public License, the rights
+     specified in Section 2(b)(1)-(2) are not Copyright and Similar
+     Rights.
+  d. Effective Technological Measures means those measures that, in the
+     absence of proper authority, may not be circumvented under laws
+     fulfilling obligations under Article 11 of the WIPO Copyright
+     Treaty adopted on December 20, 1996, and/or similar international
+     agreements.
+
+  e. Exceptions and Limitations means fair use, fair dealing, and/or
+     any other exception or limitation to Copyright and Similar Rights
+     that applies to Your use of the Licensed Material.
+
+  f. Licensed Material means the artistic or literary work, database,
+     or other material to which the Licensor applied this Public
+     License.
+
+  g. Licensed Rights means the rights granted to You subject to the
+     terms and conditions of this Public License, which are limited to
+     all Copyright and Similar Rights that apply to Your use of the
+     Licensed Material and that the Licensor has authority to license.
+
+  h. Licensor means the individual(s) or entity(ies) granting rights
+     under this Public License.
+
+  i. NonCommercial means not primarily intended for or directed towards
+     commercial advantage or monetary compensation. For purposes of
+     this Public License, the exchange of the Licensed Material for
+     other material subject to Copyright and Similar Rights by digital
+     file-sharing or similar means is NonCommercial provided there is
+     no payment of monetary compensation in connection with the
+     exchange.
+
+  j. Share means to provide material to the public by any means or
+     process that requires permission under the Licensed Rights, such
+     as reproduction, public display, public performance, distribution,
+     dissemination, communication, or importation, and to make material
+     available to the public including in ways that members of the
+     public may access the material from a place and at a time
+     individually chosen by them.
+
+  k. Sui Generis Database Rights means rights other than copyright
+     resulting from Directive 96/9/EC of the European Parliament and of
+     the Council of 11 March 1996 on the legal protection of databases,
+     as amended and/or succeeded, as well as other essentially
+     equivalent rights anywhere in the world.
+
+  l. You means the individual or entity exercising the Licensed Rights
+     under this Public License. Your has a corresponding meaning.
+
+
+Section 2 -- Scope.
+
+  a. License grant.
+
+       1. Subject to the terms and conditions of this Public License,
+          the Licensor hereby grants You a worldwide, royalty-free,
+          non-sublicensable, non-exclusive, irrevocable license to
+          exercise the Licensed Rights in the Licensed Material to:
+
+            a. reproduce and Share the Licensed Material, in whole or
+               in part, for NonCommercial purposes only; and
+
+            b. produce, reproduce, and Share Adapted Material for
+               NonCommercial purposes only.
+
+       2. Exceptions and Limitations. For the avoidance of doubt, where
+          Exceptions and Limitations apply to Your use, this Public
+          License does not apply, and You do not need to comply with
+          its terms and conditions.
+
+       3. Term. The term of this Public License is specified in Section
+          6(a).
+
+       4. Media and formats; technical modifications allowed. The
+          Licensor authorizes You to exercise the Licensed Rights in
+          all media and formats whether now known or hereafter created,
+          and to make technical modifications necessary to do so. The
+          Licensor waives and/or agrees not to assert any right or
+          authority to forbid You from making technical modifications
+          necessary to exercise the Licensed Rights, including
+          technical modifications necessary to circumvent Effective
+          Technological Measures. For purposes of this Public License,
+          simply making modifications authorized by this Section 2(a)
+          (4) never produces Adapted Material.
+
+       5. Downstream recipients.
+
+            a. Offer from the Licensor -- Licensed Material. Every
+               recipient of the Licensed Material automatically
+               receives an offer from the Licensor to exercise the
+               Licensed Rights under the terms and conditions of this
+               Public License.
+
+            b. No downstream restrictions. You may not offer or impose
+               any additional or different terms or conditions on, or
+               apply any Effective Technological Measures to, the
+               Licensed Material if doing so restricts exercise of the
+               Licensed Rights by any recipient of the Licensed
+               Material.
+
+       6. No endorsement. Nothing in this Public License constitutes or
+          may be construed as permission to assert or imply that You
+          are, or that Your use of the Licensed Material is, connected
+          with, or sponsored, endorsed, or granted official status by,
+          the Licensor or others designated to receive attribution as
+          provided in Section 3(a)(1)(A)(i).
+
+  b. Other rights.
+
+       1. Moral rights, such as the right of integrity, are not
+          licensed under this Public License, nor are publicity,
+          privacy, and/or other similar personality rights; however, to
+          the extent possible, the Licensor waives and/or agrees not to
+          assert any such rights held by the Licensor to the limited
+          extent necessary to allow You to exercise the Licensed
+          Rights, but not otherwise.
+
+       2. Patent and trademark rights are not licensed under this
+          Public License.
+
+       3. To the extent possible, the Licensor waives any right to
+          collect royalties from You for the exercise of the Licensed
+          Rights, whether directly or through a collecting society
+          under any voluntary or waivable statutory or compulsory
+          licensing scheme. In all other cases the Licensor expressly
+          reserves any right to collect such royalties, including when
+          the Licensed Material is used other than for NonCommercial
+          purposes.
+
+
+Section 3 -- License Conditions.
+
+Your exercise of the Licensed Rights is expressly made subject to the
+following conditions.
+
+  a. Attribution.
+
+       1. If You Share the Licensed Material (including in modified
+          form), You must:
+
+            a. retain the following if it is supplied by the Licensor
+               with the Licensed Material:
+
+                 i. identification of the creator(s) of the Licensed
+                    Material and any others designated to receive
+                    attribution, in any reasonable manner requested by
+                    the Licensor (including by pseudonym if
+                    designated);
+
+                ii. a copyright notice;
+
+               iii. a notice that refers to this Public License;
+
+                iv. a notice that refers to the disclaimer of
+                    warranties;
+
+                 v. a URI or hyperlink to the Licensed Material to the
+                    extent reasonably practicable;
+
+            b. indicate if You modified the Licensed Material and
+               retain an indication of any previous modifications; and
+
+            c. indicate the Licensed Material is licensed under this
+               Public License, and include the text of, or the URI or
+               hyperlink to, this Public License.
+
+       2. You may satisfy the conditions in Section 3(a)(1) in any
+          reasonable manner based on the medium, means, and context in
+          which You Share the Licensed Material. For example, it may be
+          reasonable to satisfy the conditions by providing a URI or
+          hyperlink to a resource that includes the required
+          information.
+
+       3. If requested by the Licensor, You must remove any of the
+          information required by Section 3(a)(1)(A) to the extent
+          reasonably practicable.
+
+       4. If You Share Adapted Material You produce, the Adapter's
+          License You apply must not prevent recipients of the Adapted
+          Material from complying with this Public License.
+
+
+Section 4 -- Sui Generis Database Rights.
+
+Where the Licensed Rights include Sui Generis Database Rights that
+apply to Your use of the Licensed Material:
+
+  a. for the avoidance of doubt, Section 2(a)(1) grants You the right
+     to extract, reuse, reproduce, and Share all or a substantial
+     portion of the contents of the database for NonCommercial purposes
+     only;
+
+  b. if You include all or a substantial portion of the database
+     contents in a database in which You have Sui Generis Database
+     Rights, then the database in which You have Sui Generis Database
+     Rights (but not its individual contents) is Adapted Material; and
+
+  c. You must comply with the conditions in Section 3(a) if You Share
+     all or a substantial portion of the contents of the database.
+
+For the avoidance of doubt, this Section 4 supplements and does not
+replace Your obligations under this Public License where the Licensed
+Rights include other Copyright and Similar Rights.
+
+
+Section 5 -- Disclaimer of Warranties and Limitation of Liability.
+
+  a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
+     EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
+     AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
+     ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
+     IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
+     WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
+     PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
+     ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
+     KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
+     ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
+
+  b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
+     TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
+     NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
+     INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
+     COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
+     USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
+     ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
+     DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
+     IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
+
+  c. The disclaimer of warranties and limitation of liability provided
+     above shall be interpreted in a manner that, to the extent
+     possible, most closely approximates an absolute disclaimer and
+     waiver of all liability.
+
+
+Section 6 -- Term and Termination.
+
+  a. This Public License applies for the term of the Copyright and
+     Similar Rights licensed here. However, if You fail to comply with
+     this Public License, then Your rights under this Public License
+     terminate automatically.
+
+  b. Where Your right to use the Licensed Material has terminated under
+     Section 6(a), it reinstates:
+
+       1. automatically as of the date the violation is cured, provided
+          it is cured within 30 days of Your discovery of the
+          violation; or
+
+       2. upon express reinstatement by the Licensor.
+
+     For the avoidance of doubt, this Section 6(b) does not affect any
+     right the Licensor may have to seek remedies for Your violations
+     of this Public License.
+
+  c. For the avoidance of doubt, the Licensor may also offer the
+     Licensed Material under separate terms or conditions or stop
+     distributing the Licensed Material at any time; however, doing so
+     will not terminate this Public License.
+
+  d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
+     License.
+
+
+Section 7 -- Other Terms and Conditions.
+
+  a. The Licensor shall not be bound by any additional or different
+     terms or conditions communicated by You unless expressly agreed.
+
+  b. Any arrangements, understandings, or agreements regarding the
+     Licensed Material not stated herein are separate from and
+     independent of the terms and conditions of this Public License.
+
+
+Section 8 -- Interpretation.
+
+  a. For the avoidance of doubt, this Public License does not, and
+     shall not be interpreted to, reduce, limit, restrict, or impose
+     conditions on any use of the Licensed Material that could lawfully
+     be made without permission under this Public License.
+
+  b. To the extent possible, if any provision of this Public License is
+     deemed unenforceable, it shall be automatically reformed to the
+     minimum extent necessary to make it enforceable. If the provision
+     cannot be reformed, it shall be severed from this Public License
+     without affecting the enforceability of the remaining terms and
+     conditions.
+
+  c. No term or condition of this Public License will be waived and no
+     failure to comply consented to unless expressly agreed to by the
+     Licensor.
+
+  d. Nothing in this Public License constitutes or may be interpreted
+     as a limitation upon, or waiver of, any privileges and immunities
+     that apply to the Licensor or You, including from the legal
+     processes of any jurisdiction or authority.
+
+=======================================================================
+
+Creative Commons is not a party to its public
+licenses. Notwithstanding, Creative Commons may elect to apply one of
+its public licenses to material it publishes and in those instances
+will be considered the “Licensor.” The text of the Creative Commons
+public licenses is dedicated to the public domain under the CC0 Public
+Domain Dedication. Except for the limited purpose of indicating that
+material is shared under a Creative Commons public license or as
+otherwise permitted by the Creative Commons policies published at
+creativecommons.org/policies, Creative Commons does not authorize the
+use of the trademark "Creative Commons" or any other trademark or logo
+of Creative Commons without its prior written consent including,
+without limitation, in connection with any unauthorized modifications
+to any of its public licenses or any other arrangements,
+understandings, or agreements concerning use of licensed material. For
+the avoidance of doubt, this paragraph does not form part of the
+public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
+

vartrace-0.1.0/PKG-INFO

@@ -0,0 +1,146 @@
+Metadata-Version: 2.5
+Name: vartrace
+Version: 0.1.0
+Summary: Estimates whether a variant seen in single-cell RNA-seq is present in the genome
+Author-email: Kamen Yovchev <kamen.yovchev@gmail.com>
+License-Expression: PolyForm-Noncommercial-1.0.0 AND CC-BY-NC-4.0
+License-File: LICENSE
+License-File: LICENSE-MODELS
+Requires-Python: >=3.12
+Requires-Dist: altair
+Requires-Dist: joblib==1.5.3
+Requires-Dist: numpy==2.4.6
+Requires-Dist: pandas==3.0.5
+Requires-Dist: requests
+Requires-Dist: scikit-learn==1.9.0
+Requires-Dist: streamlit
+Requires-Dist: xgboost==3.4.0
+Description-Content-Type: text/markdown
+
+# VarTrace
+
+VarTrace estimates, for each variant observed in single-cell RNA sequencing, the
+probability that the variant is not present in the genome of that cell. It works
+from the RNA data alone, without paired DNA sequencing.
+
+
+## Why
+
+A variant seen in RNA may be present in the genome, or it may arise only at the
+RNA level. Telling the two apart normally requires sequencing the DNA of the same
+cell, which is expensive and often not possible. The common shortcut, checking
+whether the variant is listed in public databases, misclassifies a large share of
+cases in both directions.
+
+VarTrace answers the question from the RNA data and returns a calibrated
+probability rather than a yes or no. A score of 0.87 means that of a hundred
+variants scored that way, about 87 really are absent from the genome.
+
+
+## Installing
+
+    pipx install vartrace
+
+Or, for the latest state of the source:
+
+    pipx install "git+https://codeberg.org/KamenYovchev/vartrace.git"
+
+The trained models come with the package and the web interface is included, so
+nothing else has to be downloaded or installed separately.
+
+
+## Using it
+
+Run it with nothing after it and the web interface opens in the browser. It
+listens only on your own machine, so the files you load stay on it.
+
+    vartrace
+
+Give it files instead and it works from the command line, one file per cell or
+one file holding many cells:
+
+    vartrace cell_01.vcf
+    vartrace cells/*.tsv --threshold 0.867 --output results.tsv
+
+Options:
+
+    --threshold     0.5 by default. 0.867 is the high confidence mode, where
+                    precision is about 0.99 at the cost of some recall.
+    --no-annotate   do not ask Ensembl for dbSNP and gnomAD when the input
+                    carries no annotation of its own.
+    --output        where to write the table. A second file with the same name
+                    and .info.txt records what produced it.
+
+
+## Input
+
+A plain VCF, as it comes from the variant caller, or a table annotated with
+ANNOVAR, where the VCF fields sit in the Otherinfo columns.
+
+A VCF may hold one sample or many. One column per cell barcode is read as many
+cells, and a cell is counted for a variant only when its genotype or its allele
+depth says it carries it.
+
+Only biallelic single base substitutions are used, because that is what the
+models were trained on. Anything else is counted and skipped, and the count is
+reported.
+
+If the input carries no database annotation, VarTrace looks up dbSNP and gnomAD
+through the public Ensembl service. That needs an internet connection and can be
+switched off. Of the five database features these two carry nearly all of the
+weight, which is why the other two are used when present but never fetched.
+
+
+## Output
+
+A table with one row per variant: the cell, the position, the alleles, the
+score, the call at the chosen threshold, and which model was used.
+
+Alongside it a short record of what produced those numbers, including the model
+file and its fingerprint, and where the annotation came from.
+
+The tool also states in words why it chose the model it did, for example that
+the input had dbSNP and gnomAD but not REDIportal or COSMIC.
+
+
+## The models
+
+Five models come with the package and one is chosen automatically from what the
+input supports. No database annotation at all, or all four databases, is served
+by a model trained for exactly that case, with or without the cross-cell
+features depending on whether more than one cell was given. Anything in between
+goes to a model trained with feature groups withheld at random, which is the
+only one that can take a partial input.
+
+Each model carries a description in JSON next to it: the algorithm, its
+settings, the features it expects in order, what it was trained on, and its
+validation metrics.
+
+
+## Scope and limitations
+
+The models were trained on 45 single cells from three cell lines, sequenced with
+one technology, with paired DNA sequencing as the ground truth. They have not
+been validated on primary tissue or on other protocols.
+
+The score answers one question: is the variant present in the genome. It does
+not say which biological process produced a variant that is absent from it.
+
+The models were trained on gnomAD as ANNOVAR supplies it. When VarTrace fetches
+the frequencies from Ensembl instead, the release may differ; which one answered
+is recorded in the output.
+
+
+## Licence
+
+Code: PolyForm Noncommercial License 1.0.0, see LICENSE.
+Trained models: Creative Commons Attribution-NonCommercial 4.0, see
+LICENSE-MODELS.
+
+Free for research and any other non-commercial use. Commercial use is not
+permitted.
+
+
+## Citation
+
+To follow.