From a63b37089ea896e33ebb6d42a23f335d80b7332d Mon Sep 17 00:00:00 2001
From: vladijouan <2212-vladijouan@users.noreply.git.imp.fu-berlin.de>
Date: Thu, 25 May 2023 13:40:09 +0000
Subject: [PATCH] Update README.md
---
README.md | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/README.md b/README.md
index 6936391..6decd42 100644
--- a/README.md
+++ b/README.md
@@ -141,3 +141,16 @@
rm tmp*;
done < list_of_chromosomes.txt`
+#IBIS IBD segments
+
+`vcftools --gzvcf 1stbatch_higherquality_snps.vcf.gz --out highQ_snps_DP15 --recode --recode-INFO-all --minDP 15 --maxDP 100`
+
+`bcftools view -Oz -o highQ_snps_DP15.recode.filtered.vcf.gz -g ^miss highQ_snps_DP15.recode.vcf`
+
+`tabix highQ_snps_DP15.recode.filtered.vcf.gz`
+
+`bcftools view -r 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 -Oz -o highQ_snps_DP15.recode.filtered_20chr.vcf.gz highQ_snps_DP15.recode.filtered.vcf.gz`
+
+`plink2 --vcf highQ_snps_DP15.recode.filtered_20chr.vcf.gz --make-bed --out DP15.filtered`
+
+`$IBISPATH/ibis -bfile DP15.filtered -noFamID -o DP15.filtered -printCoef -a 0.0`
--
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