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===SNP matrix=== * Run MasterBisReadMapper with variant calling. Since I already have the sam files to give as input, MasterBisReadMapper will not need to re-map the data. * Homozygous SNPs are also called at dbSNP138 positions. * After getting the *filtered.SNP.txt files, generate the tped and tfam files for plink. /home/dinh/scripts/BisReadMapper/src/snp2tfiles.pl * Merge tped files into the large tped matrix for plink. /home/dinh/scripts/BisReadMapper/src/tped-merge.pl * Run plink: /home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --geno 0 --maf 0.01 --tfile monod_141216 --recode --transpose --out monod_141216.plink **** 92639 SNPs failed missingness test ( GENO > 0 ) **** 84830 SNPs failed frequency test ( MAF < 0.01 ) 993 SNPs left. /home/nplongth/softwares/plink-1.07-x86_64/plink --noweb --tfile monod_141216.plink --cluster --matrix * the plink.mibs fie is a N x N matrix of genome-wide average IBS pairwise identities * use R to plot the dendrogram: A = read.table("plink.mibs", F) labels = read.table("monod_141216.plink.tfam",F) colnames(A) = labels$V2 plot(hclust(as.dist(1-A)), main="plink.mibs") dev.off() * SNPs dendrogram: [[File:monod_capture_plink_mibs.png | 800px]]
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