Add VCEP Documentation (#199)

docs/acmg_seqvars_implementation.rst → docs/acmg_seqvar_implementation.rst

@@ -1,4 +1,4 @@
-.. _acmg_seqvars_implementation:
+.. _acmg_seqvar_implementation:
 
 ===============================================================
 Implementation of different ACMG criteria for sequence variants
@@ -20,15 +20,6 @@ For sequence variants:
     :show-inheritance:
     :private-members:
 
-For structural variants:
-
-.. automodule:: src.strucvar.auto_pvs1
-    :members:
-    :inherited-members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-
 -----------
 PS1 and PM5
 -----------

docs/acmg_seqvars_criteria.rst

@@ -251,10 +251,6 @@ Criteria
 PVS1 (null variant)
 ===================
 
-.. note::
-
-    For full information visit the dedicated section of :ref:`PVS1 Algorithm <acmg_pvs1_algorithm>`.
-
 Original Definition
 -------------------
 
@@ -1132,4 +1128,4 @@ Notes
 Bibliography
 ============
 
-.. footbibliography::
+.. footbibliography::

docs/acmg_strucvar_implementation.rst

@@ -0,0 +1,22 @@
+.. _acmg_strucvar_implementation:
+
+===============================================================
+Implementation of different ACMG criteria for sequence variants
+===============================================================
+
+This section contains the internal building blocks for the
+implementation of the different ACMG criteria for sequence variants.
+
+
+----
+PVS1
+----
+
+For structural variants:
+
+.. automodule:: src.strucvar.auto_pvs1
+    :members:
+    :inherited-members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:

docs/auto_acmg_implementation.rst

@@ -0,0 +1,62 @@
+.. _auto_acmg_implementation:
+
+=============================
+Auto-ACMG Implementation
+=============================
+
+
+Auto-ACMG operates through a structured process to determine the most appropriate predictor based on
+the type and context of the genetic variant being analyzed. This document describes the general
+workflow and the mechanisms behind the decisions that auto-acmg makes to predict the classification
+of genetic variants.
+
+Workflow Overview
+-----------------
+
+1. **Variant Resolution**:
+   The first step involves determining the type of genetic variant. If the variant is recognized as
+   a sequence variant (seqvar), auto-acmg employs the SeqVar default predictor. For structural
+   variants (strucvar), the StrucVar default predictor is utilized, which primarily evaluates the
+   PVS1 criteria.
+
+2. **Gene-Specific Evaluation**:
+   For seqvars, auto-acmg checks if the variant is associated with any gene that has a specific
+   Variant Curation Expert Panel (VCEP) implementation. If a specific VCEP is applicable, auto-acmg
+   will switch to the corresponding VCEP predictor for that gene to leverage expert-specified
+   evaluation criteria and thresholds.
+
+   - **SeqVar Implementation**: If no specific VCEP is applicable, the default SeqVar predictor is
+     used. The implementation details of the default SeqVar predictor are described in
+     :ref:`acmg_seqvar_implementation`.
+
+3. **Structural Variants**:
+   For structural variants, the default predictor primarily evaluates the PVS1 criteria. You can
+   find the implementation of the default StrucVar predictor in
+   :ref:`acmg_strucvar_implementation`.
+
+VCEP-Specific Overrides
+-----------------------
+
+Each VCEP-specific predictor may override certain logic or thresholds of the Default Predictor:
+
+- **Threshold Adjustments**: Some VCEP implementations may just adjust thresholds for criteria like
+  PP3 or BP4 and don't override the prediction logic.
+
+- **Prediction Logic Changes**: Other VCEPs may override the entire logic for certain criteria. This
+  can include changing how predictions are made based on the variant's effects on protein function,
+  splicing, or other molecular mechanisms.
+
+For a detailed overview of how specific VCEP predictors modify or extend the default behavior, you
+can review the source code on the GitHub repository under ``src/vcep`` and for the details refer to
+the `ClinGen VCEP Criteria Specification Registry <https://cspec.genome.network/cspec/ui/svi/>`__.
+
+Link to Source Code
+-------------------
+
+Further details and the actual implementation of both default and VCEP-specific predictors can be
+accessed through our `GitHub <https://github.com/auto-acmg/src/vcep>`_ repository.
+
+.. note::
+   The implementation specifics for each VCEP can vary significantly based on the gene and
+   associated conditions. It is recommended to consult the individual VCEP documentation and the
+   source code for precise information on how each gene-specific predictor is implemented.

docs/index.rst

@@ -1,20 +1,56 @@
 .. _index:
 
-=========
-auto-acmg
-=========
+=====================
+Welcome to auto-acmg
+=====================
+
+Auto-acmg is a comprehensive software suite designed for the automatic prediction of ACMG (American
+College of Medical Genetics and Genomics) criteria for the evaluation of sequence variants and copy
+number variations (CNVs) in genetic data. Its primary function is to assist geneticists and
+researchers by providing a systematic approach to classify genetic variants according to established
+guidelines. More information to the guidelines can be found at the :ref:`acmg_seqvars_criteria` and
+:ref:`acmg_seqvars_details` sections.
+
+Key Features
+------------
+
+- **Variant Classification**: Auto-acmg classifies single nucleotide variants (SNVs) and CNVs based
+    on ACMG guidelines, enhancing the accuracy and consistency of genetic interpretations.
+
+- **Implementation of ACMG Criteria**: It supports a range of criteria including PVS1, PS1, PM1,
+    PM2, PM4, PM5, PP2, PP3, BA1, BS1, BS2, BP1, BP3, BP4 and BP7, allowing users to
+    assess the pathogenicity of variants in a comprehensive manner.
+
+- **VCEP Specifications**: The software is designed to adhere to Variant Curation Expert Panel
+    (VCEP) specifications, ensuring that each prediction is tailored to the specific genes and
+    conditions studied by expert panels.
+
+- **Extensible and Adaptable**: Auto-acmg can be customized and extended to accommodate new criteria
+    and guidelines as genetic science evolves.
+
+
+Getting Started
+---------------
+
+If you are new to auto-acmg, a good starting point is the :ref:`usage` section which provides
+detailed instructions on how to use the software effectively.
+
+If you are interested in contributing to auto-acmg, please refer to the :ref:`dev_quickstart`
+section.
+
+Also pay attention to the :ref:`auto_acmg_implementation` section to understand how auto-acmg
+works internally.
 
-Auto-acmg is a program for automatical prediction of ACMG criteria for sequence variants.
-If you want to **use** auto-acmg, the best place is to start at :ref:`usage`.
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
+   auto_acmg_implementation
    acmg_seqvars_details
    acmg_seqvars_criteria
-   acmg_seqvars_implementation
-   acmg_pvs1
+   acmg_seqvar_implementation
+   acmg_strucvar_implementation
 
 .. toctree::
     :maxdepth: 2