Update README.md

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`