Difference between revisions of "Phewas"
From Crop Genomics Lab.
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[SNP imputation] | [SNP imputation] | ||
정순천 박사님 논문에 나온 781 accession 중 G.max만 418개 골라서 vcf 만듦, '/'를 '|'로 : 418_gmax_accession.vcf | 정순천 박사님 논문에 나온 781 accession 중 G.max만 418개 골라서 vcf 만듦, '/'를 '|'로 : 418_gmax_accession.vcf | ||
− | + | https://figshare.com/projects/Soybean_haplotype_map_project/76110 | |
beagle 5.1 이용하여 imputation | beagle 5.1 이용하여 imputation | ||
java -Xmx4g -jar /data/programs/beagle.18May20.d20.jar gt=./CMV_final.vcf ref=../data_collection/418_gmax_accession.vcf out=./beagle_test_418_CMV | java -Xmx4g -jar /data/programs/beagle.18May20.d20.jar gt=./CMV_final.vcf ref=../data_collection/418_gmax_accession.vcf out=./beagle_test_418_CMV |
Latest revision as of 07:29, 19 February 2021
[GWAS data collection] GRIN에서 soy50k로 찍은 GWAS data 수집 phenotype 있는 accession들만 vcf 정리, mitochondria, scaffold SNP 빼기 : CMV_phenotype.vcf.mtX2.scaX Plink 이용하여 IBD 계산후 0.98로 cut, missing이랑 hetero 골라내기, '/'를 '|'로 : CMV_final.vcf
/data/program/plink --vcf ./CMV_phenotype.vcf.mtX2.scaX --genome remove_IBD_less_0,98.py
[SNP imputation] 정순천 박사님 논문에 나온 781 accession 중 G.max만 418개 골라서 vcf 만듦, '/'를 '|'로 : 418_gmax_accession.vcf
https://figshare.com/projects/Soybean_haplotype_map_project/76110
beagle 5.1 이용하여 imputation
java -Xmx4g -jar /data/programs/beagle.18May20.d20.jar gt=./CMV_final.vcf ref=../data_collection/418_gmax_accession.vcf out=./beagle_test_418_CMV
[GEMMA] GEMMA 이용하여 MLM으로 phe:gen association보기 phenotype data : CMV_phenotype_O.txt