diff --git a/README.md b/README.md index 6936391f7688f0caa63265758378b531f02e41cf..6decd42b164d81a994c4022b3eb3db9ccde0c0a3 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`