From 272b07727a5db25b689556a3eba2561163131da1 Mon Sep 17 00:00:00 2001
From: "Helia (Helyaneh) Ziaei Jam"
 <79483655+heliziii@users.noreply.github.com>
Date: Tue, 28 May 2024 20:39:29 -0700
Subject: [PATCH] Update README.md

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3000a19..f287cd4 100644
--- a/README.md
+++ b/README.md
@@ -135,7 +135,7 @@ TRs imputed from 3,202 1kGP samples.
 
 Total 70,692,015 variants + 1,091,550 TR markers.
 
-All the coordinates are based on the hg38 human reference genome.
+All the coordinates are based on **hg38** human reference genome.
 
 ### Availability
 
@@ -194,6 +194,8 @@ java -Xmx4g -jar beagle.version.jar \
             out=imputed_TR_SNPs
 ```
 
+Please use the [beagle version 5.4](https://github.com/gymreklab/1000Genomes-TR-Analysis/raw/main/phasing/validation/beagle.19Apr22.7c0.jar) for this analysis as we had issued with the newer versions of Beagle and we are right now communicating it with Beagle developers.
+
 ## Additional resources
 
 Per locus summary statistics can be downloaded from [here](https://ensemble-tr.s3.us-east-2.amazonaws.com/tables/repeat_tables.zip). Each table has information on coordinates, repeat unit sequence, and potential overlap with genes listed in GENCODE v22 for repeats in EnsembleTR catalog.