Add QC swap changes

docs/contact.md

@@ -8,7 +8,7 @@ hide:
 
 The source code of Michigan Imputation Server 2 is  available on [GitHub](https://github.com/genepi/imputationserver2). Feel free to create issues and pull requests. Before contacting us, please have a look at the [FAQ page](faq) first. 
 
-## Michigan Imputation Server Team
+## Michigan Imputation Server 2 Team
 
 Michigan Imputation Server provides a free genotype imputation service using Minimac4. You can upload phased or unphased GWAS genotypes and receive phased and imputed genomes in return. For all uploaded data sets an extensive QC is performed.
 

docs/getting-started.md

@@ -136,7 +136,7 @@ In this step, we check each variant and exclude it if it meets any of the follow
 All filtered variants are listed in a file called `statistics.txt`, which can be downloaded by clicking the provided link. More information about our QC pipeline can be found [here](/pipeline).
 
 !!! important
-    Due to changes in Minimac 4, Michigan Imputation Server 2 now includes filtering and checks for allele swaps. For more information, please read HERE.
+    Due to changes in Minimac 4, Michigan Imputation Server 2 now includes filtering and checks for allele swaps. For more information, please click [here](./qc-allele-swaps.md).
 
 ![](images/quality-control02.png)
 

docs/index.md

@@ -23,7 +23,7 @@ Please cite this paper if you use Michigan Imputation Server 2:
 
 <p>
     <small class="text-muted"><i class="far fa-calendar-alt"></i> 19 September 2024</small><br>
-    We have migrated to a new architecture and released Michigan Imputation Server 2. Please note the change regarding allele swaps in Minimac4, which may affect your QC.
+   We have successfully migrated to a new architecture and released Michigan Imputation Server 2. Please note the major change regarding allele swaps! <a href="./qc-allele-swaps" target="_blank"> <br> Learn more.</a>
 </p>
 
 <p>

docs/qc-allele-swaps.md

@@ -0,0 +1,27 @@
+# Changes in Allele Swaps Handling in Imputation Server 2.0
+
+With the update to the latest Minimac4 version, we have modified the default handling of allele swaps in Michigan Imputation Server 2. 
+
+## Overview of Changes
+
+In previous versions of the server, swapped reference and alternate alleles were automatically corrected, with only ambiguous SNPs being filtered out. To improve genotype quality and avoid errors from incorrectly genotyped variants, the handling of allele swaps has now been updated.
+
+## Key Changes
+
+- **Previous Behavior**: Allele swaps were automatically corrected, with only ambiguous SNPs being filtered out.
+- **New Behavior**: With the update, the server now enforces stricter quality control. The system allows up to 100 allele swaps during processing. If more than 100 allele swaps are detected, the quality control process will fail, stopping the imputation process to prevent poor genotype quality.
+
+## Impact on Data Submissions
+
+This update may cause failures in submissions that were previously accepted but now exceed the 100-allele swap threshold.
+
+## Recommendations
+
+To avoid imputation quality issues and ensure your data meets the new allele swaps threshold:
+
+- We recommend using tools such as Will Rayner’s tool to check for and correct allele switches in your dataset.
+
+- This will ensure that issues such as **strand or allele flips** are resolved before submission, helping your data meet the new quality standards.
+
+
+Please follow these steps to verify your data before submitting it to Imputation Server 2.

mkdocs.yml

@@ -35,6 +35,7 @@ nav:
 - Genotype Imputation:
   - Getting Started: getting-started.md
   - Data Preparation: prepare-your-data.md
+  - Changes in Allele Swap Handling: qc-allele-swaps.md
   - Pipeline Overview: pipeline.md
   - Security: data-sensitivity.md
   - FAQ: faq.md