Update README.md with WDL Workflow for Extracting Variant Information

README.md

@@ -1 +1,54 @@
-# get-variant-info
+# WDL Workflow for Extracting Variant Information
+
+[![Open](https://img.shields.io/badge/Open-Dockstore-blue)](https://dockstore.org/workflows/github.com/IMCM-OX/get-variant-info:main?tab=info)  
+![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/IMCM-OX/get-variant-info/publish.yml)  
+![GitHub release (with filter)](https://img.shields.io/github/v/release/IMCM-OX/get-variant-info)  
+
+> [!TIP]
+> To import the workflow into your Terra workspace, click on the above Dockstore badge, and select 'Terra' from the 'Launch with' widget on the Dockstore workflow page.
+
+
+This repository contains a WDL (Workflow Description Language) workflow for extracting information from a set of imputed VCF files using a list of query variants or sample IDs.
+
+The workflow extracts the following information:
+
+- Chromosome
+- Position
+- Reference allele
+- Alternate allele
+- Allele frequency (AF)
+- Minor allele frequency (MAF)
+- Imputation accuracy (R2)
+- Empirical R-square (ER2)
+- Genotype (GT)
+- Estimated Alternate Allele Dosage (DS)
+- Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1 (GP)
+
+The output is a set of files containing the extracted information.
+
+## Workflow Inputs
+
+- `query_variants`: A tab-delimited file with a list of query variants. Each line should be formatted as: Chromosome, Pos, ID, Ref, Alt. (required)
+- `query_samples`: A file with a list of sample IDs. Each line should contain one sample ID. (optional)
+- `imputed_vcf`: Array of imputed VCF files and their indices. VCF files should be in .vcf.gz format and indices in CSI or TBI format. (required)
+- `prefix`: Prefix for the output files. (required)
+- `extract_item`: A string specifying the information to extract from the FORMAT field of the VCF file. The available choices are GT, DS, and GP. Please provide as a comma-separated string. (required)
+
+## Workflow Outputs
+
+- `snp_info`: File containing SNP information.
+- `genotype_info`: Optional file containing genotype information.
+- `dosage_info`: Optional file containing estimated alternate allele dosage information.
+- `geno_prob_info`: Optional file containing estimated posterior probabilities for genotypes.
+
+
+## Components
+
+- **Python packages**
+  - pysam
+  - pandas
+  - argparse
+- **Tools**
+  - bcftools
+- **Containers**
+  - ghcr.io/IMCM-OX/get-variant-info