From bbf58cbf38d310e724e05c003e820a776833942a Mon Sep 17 00:00:00 2001
From: Oleksandr Frei <oleksandr.frei@gmail.com>
Date: Wed, 17 Dec 2025 13:11:35 +0100
Subject: [PATCH 1/3] Update README with .snps file generation instructions

Added instructions for generating .snps files using SLURM.
---
 README.md | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/README.md b/README.md
index 475c83e..d9b0b76 100644
--- a/README.md
+++ b/README.md
@@ -306,6 +306,22 @@ export MIXER_PY="singularity exec --home pwd:/home ${MIXER_SIF} python /tools/mi
 ${MIXER_PY} ld --bfile chr${CHR} --r2min 0.01 --ldscore-r2min 0.0001 --ld-window-kb 10000 --out chr${CHR}.ld
 ```
 
+After finishing previous jobs, run the following to generate .snps files:
+```
+#SBATCH --time=48:00:00
+#SBATCH --ntasks=1
+#SBATCH --mem-per-cpu=8000M
+#SBATCH --cpus-per-task=8
+#SBATCH --array=1-20
+
+export REPI=${SLURM_ARRAY_TASK_ID}
+export SEED=$((SLURM_ARRAY_TASK_ID + 1000))
+export MIXER_SIF=mixer.sif
+export MIXER_PY="singularity exec --home pwd:/home ${MIXER_SIF} python /tools/mixer/precimed/mixer.py"
+
+${MIXER_PY} snps --bim-file chr@.bim --ld-file chr@.ld --r2 0.8 --maf 0.05 --subset 2000000 --out chr_pr une_maf0p05_rand2M_r2p8.${REPI}.snps --seed $SEED
+```
+
 For full command-line reference, see ``mixer.py ld --help``.
 
 Analyses in [GSA-MiXeR publication](https://www.nature.com/articles/s41588-024-01771-1) are based on UKB and HRC reference panen, partly shared here:

From d11e84646a42c777f41fcb03f3e39c789d019000 Mon Sep 17 00:00:00 2001
From: Oleksandr Frei <oleksandr.frei@gmail.com>
Date: Wed, 17 Dec 2025 13:23:20 +0100
Subject: [PATCH 2/3] Update README.md

---
 README.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/README.md b/README.md
index d9b0b76..4f0caf8 100644
--- a/README.md
+++ b/README.md
@@ -305,6 +305,12 @@ export MIXER_PY="singularity exec --home pwd:/home ${MIXER_SIF} python /tools/mi
 
 ${MIXER_PY} ld --bfile chr${CHR} --r2min 0.01 --ldscore-r2min 0.0001 --ld-window-kb 10000 --out chr${CHR}.ld
 ```
+Note that the reference should be generated from unrelated individuals, e.g. using "king --unrelated --degree 2", or any alternative way. You should check .log output of "mixer.py ld" to see how that the number of LD r2 elements decrease for SNPs in distant blocks, as in [this example]()https://media.githubusercontent.com/media/comorment/mixer/refs/heads/main/reference/hrc_EUR_qc/hrc_chr10_EUR_qc.run1.ld.log. 
+```
+ processed  block 1x1 of 75x75, 2019080 new r2 elements found, ...
+ processed  block 1x2 of 75x75, 99291 new r2 elements found, ...
+ processed  block 1x3 of 75x75, 624 new r2 elements found, ...
+```
 
 After finishing previous jobs, run the following to generate .snps files:
 ```

From bd1fdb4d9f120dc66efd10368180f4df4f178d74 Mon Sep 17 00:00:00 2001
From: Oleksandr Frei <oleksandr.frei@gmail.com>
Date: Wed, 17 Dec 2025 13:23:59 +0100
Subject: [PATCH 3/3] Fix link formatting in README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 4f0caf8..b7372d2 100644
--- a/README.md
+++ b/README.md
@@ -305,7 +305,7 @@ export MIXER_PY="singularity exec --home pwd:/home ${MIXER_SIF} python /tools/mi
 
 ${MIXER_PY} ld --bfile chr${CHR} --r2min 0.01 --ldscore-r2min 0.0001 --ld-window-kb 10000 --out chr${CHR}.ld
 ```
-Note that the reference should be generated from unrelated individuals, e.g. using "king --unrelated --degree 2", or any alternative way. You should check .log output of "mixer.py ld" to see how that the number of LD r2 elements decrease for SNPs in distant blocks, as in [this example]()https://media.githubusercontent.com/media/comorment/mixer/refs/heads/main/reference/hrc_EUR_qc/hrc_chr10_EUR_qc.run1.ld.log. 
+Note that the reference should be generated from unrelated individuals, e.g. using "king --unrelated --degree 2", or any alternative way. You should check .log output of "mixer.py ld" to see how that the number of LD r2 elements decrease for SNPs in distant blocks, as in [this example](https://media.githubusercontent.com/media/comorment/mixer/refs/heads/main/reference/hrc_EUR_qc/hrc_chr10_EUR_qc.run1.ld.log)
 ```
  processed  block 1x1 of 75x75, 2019080 new r2 elements found, ...
  processed  block 1x2 of 75x75, 99291 new r2 elements found, ...