0-99 a: screen -r 65455 anapop 0-99 a: screen -r 71910 plots 100-199 b: screen -r 71925 200-299 c: screen -r 39161 300-399 d: screen -r 39178 400-499 e: screen -r 39189 500-599 f: screen -r 39206 600-639 g: screen -r 39218 nice -19 /system/apps/biosoft/R-2.14.0/bin/R source("/seppdata/sepp/linkage/release/split/ana_ancest.R") source("/seppdata/sepp/linkage/release/split/ana_popratio_all.R") source("/seppdata/sepp/linkage/release/split/dups.R") source("/seppdata/sepp/linkage/release/split/extract_pos_all.R") nice -19 /system/apps/biosoft/R-2.14.0/bin/R source("/seppdata/sepp/linkage/release/split/ana_denisova.R") source("/seppdata/sepp/linkage/release/split/ana_neander.R") #################################################################### vcf <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/T_hg19_1000g.Genotypes.vcf",sep="\t") hg19 <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/hg191000.bed",sep="\t") hg19M <- paste(as.character(hg19[,1]),as.character(as.numeric(hg19[,2])),sep="") vcfM <- paste("chr",as.character(vcf[,1]),as.character(as.numeric(vcf[,2])),sep="") mm <- match(vcfM,hg19M,nomatch=0) ma <- which(mm>0) adds <- vcf[ma,5] refs <- vcf[ma,4] pos <- hg19[mm[ma],4] l <- length(hg19[,4]) ad1 <- rep("-",l) ref1 <- rep("-",l) ad1[mm[ma]] <- as.character(adds) ref1[mm[ma]] <- as.character(refs) denisovaHg19 <- cbind(hg19,ref1,ad1) denisovaHg19[1:100,] save(denisovaHg19,file="denisovaHg19.Rda") > table(denisovaHg19$ad1) - A,C,G A,C,T A,C,X A,G,C A,G,T A,G,X A,T,C 169327 1 9 2131 5 2 1074 5 A,T,G A,T,X A,X C,A,G C,A,T C,A,X C,G,A C,G,T 9 5220 1198757 10 10 5336 11 5 C,G,X C,T,A C,T,G C,T,X C,X G,A,C G,A,T G,A,X 1489 15 8 3424 807254 5 17 3673 G,C,A G,C,T G,C,X G,T,A G,T,C G,T,X G,X T,A,C 6 3 1700 11 14 5032 808121 7 T,A,G T,A,X T,C,A T,C,G T,C,X T,G,A T,G,C T,G,X 12 5752 8 2 1162 10 7 2355 T,X X 1199518 36442515 chr1 <- which(denisovaHg19$V1=="chr1") length(chr1) [1] 3201157 > denisovaHg19Chr1 <- denisovaHg19[chr1,] save(denisovaHg19Chr1,file="denisovaHg19Chr1.Rda") ta <- table(denisovaHg19Chr1$ad1) ta - A,C,G A,C,T A,C,X A,G,C A,G,T A,G,X A,T,C A,T,G A,T,X 10632 0 0 200 1 0 85 0 1 404 A,X C,A,G C,A,T C,A,X C,G,A C,G,T C,G,X C,T,A C,T,G C,T,X 93586 0 1 414 1 0 131 0 0 287 C,X G,A,C G,A,T G,A,X G,C,A G,C,T G,C,X G,T,A G,T,C G,T,X 63639 0 3 276 0 0 153 0 0 390 G,X T,A,C T,A,G T,A,X T,C,A T,C,G T,C,X T,G,A T,G,C T,G,X 63833 3 0 429 1 1 79 0 1 179 T,X X 93921 2872506 #################################################################### hg18 <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/hg181000.bed",sep="\t") hg19 <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/hg191000.bed",sep="\t") vcf <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/NeandertalGenotypes.vcf",sep="\t") hg18M <- paste(as.character(hg18[,1]),as.character(as.numeric(hg18[,2])),sep="") vcfM <- paste(as.character(vcf[,1]),as.character(as.numeric(vcf[,2])),sep="") mm <- match(vcfM,hg18M,nomatch=0) ma <- which(mm>0) adds <- vcf[ma,5] refs <- vcf[ma,4] pos <- hg18[mm[ma],4] mp <- match(pos,hg19[,4],nomatch=0) mpa <- which(mp>0) adds <- adds[mpa] refs <- refs[mpa] mp <- mp[mpa] l <- length(hg19[,4]) ad1 <- rep("-",l) ref1 <- rep("-",l) ad1[mp] <- as.character(adds) ref1[mp] <- as.character(refs) neanderHg19 <- cbind(hg19,ref1,ad1) neanderHg19[1:100,] save(neanderHg19,file="neanderHg19.Rda") > levels(neanderHg19$ad1) [1] "-" "A,C,G" "A,C,T" "A,C,X" "A,G,C" "A,G,T" "A,G,X" "A,T,C" "A,T,G" [10] "A,T,X" "A,X" "C,A,G" "C,A,T" "C,A,X" "C,G,A" "C,G,T" "C,G,X" "C,T,A" [19] "C,T,G" "C,T,X" "C,X" "G,A,C" "G,A,T" "G,A,X" "G,C,A" "G,C,T" "G,C,X" [28] "G,T,A" "G,T,C" "G,T,X" "G,X" "T,A,C" "T,A,G" "T,A,X" "T,C,A" "T,C,G" [37] "T,C,X" "T,G,A" "T,G,C" "T,G,X" "T,X" "X" chr1 <- which(neanderHg19$V1=="chr1") length(chr1) neanderHg19Chr1 <- neanderHg19[chr1,] save(neanderHg19Chr1,file="neanderHg19Chr1.Rda") ta <- table(neanderHg19Chr1$ad1) ta - A,C,G A,C,T A,C,X A,G,C A,G,T A,G,X A,T,C A,T,G A,T,X 1069131 0 0 81 1 0 51 1 0 98 A,X C,A,G C,A,T C,A,X C,G,A C,G,T C,G,X C,T,A C,T,G C,T,X 53106 0 2 99 0 0 44 1 1 171 C,X G,A,C G,A,T G,A,X G,C,A G,C,T G,C,X G,T,A G,T,C G,T,X 36745 0 0 182 0 0 48 0 1 92 G,X T,A,C T,A,G T,A,X T,C,A T,C,G T,C,X T,G,A T,G,C T,G,X 36989 0 1 125 1 0 75 0 0 101 T,X X 54109 1949901 sum(ta) sum(ta[2:41]) > sum(ta) [1] 3201157 > > sum(ta[2:41]) [1] 182125 data <- read.table("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes_annot.txt",skip=2) length(data[[10]]) [1] 3201157 > a1 <- which(data[[10]]<0.05) length(a1) [1] 2596777 neanderHg19Chr1Rare <- neanderHg19[a1,] tar <- table(neanderHg19Chr1Rare$ad1) tar sum(tar) sum(tar[2:41]) > tar - A,C,G A,C,T A,C,X A,G,C A,G,T A,G,X A,T,C A,T,G A,T,X 853706 0 0 32 0 0 13 0 0 59 A,X C,A,G C,A,T C,A,X C,G,A C,G,T C,G,X C,T,A C,T,G C,T,X 27968 0 1 44 0 0 14 1 0 46 C,X G,A,C G,A,T G,A,X G,C,A G,C,T G,C,X G,T,A G,T,C G,T,X 10106 0 0 48 0 0 18 0 1 36 G,X T,A,C T,A,G T,A,X T,C,A T,C,G T,C,X T,G,A T,G,C T,G,X 10238 0 0 89 1 0 30 0 0 58 T,X X 28594 1665674 > > sum(tar) [1] 2596777 ratio rare: 3201157 2596777/3201157 [1] 0.8111995 > > sum(tar[2:41]) [1] 77397 > neandertal snps all: 182125 neandertal snps rare: 77397 ratio rare neandertal diffs: 77397/182125 > 77397/182125 [1] 0.4249664