Inbred mouse SV genotyping ERP011529
Mark Ziemann & Kingsley Isaac Ogamanya
2021-09-30
Loading the data
ERX1059306_svtyper.vcf ERX1059307_svtyper.vcf ERX1059308_svtyper.vcf ERX1059309_svtyper.vcf ERX1059310_svtyper.vcf ERX1059311_svtyper.vcf ERX1059312_svtyper.vcf ERX1059313_svtyper.vcf ERX1059314_svtyper.vcf
# reading in the GFF files
gff <- read.table("Mus_musculus.GRCm38.98.gff3", sep = "\t", quote = "")
v06 <- readVcf("VCF_ERP011529_GRCm39/ERX1059306_svtyper.vcf", "GRCm39")
v07 <- readVcf("VCF_ERP011529_GRCm39/ERX1059307_svtyper.vcf", "GRCm39")
v08 <- readVcf("VCF_ERP011529_GRCm39/ERX1059308_svtyper.vcf", "GRCm39")
v09 <- readVcf("VCF_ERP011529_GRCm39/ERX1059309_svtyper.vcf", "GRCm39")
v10 <- readVcf("VCF_ERP011529_GRCm39/ERX1059310_svtyper.vcf", "GRCm39")
v11 <- readVcf("VCF_ERP011529_GRCm39/ERX1059311_svtyper.vcf", "GRCm39")
v12 <- readVcf("VCF_ERP011529_GRCm39/ERX1059312_svtyper.vcf", "GRCm39")
v13 <- readVcf("VCF_ERP011529_GRCm39/ERX1059313_svtyper.vcf", "GRCm39")
v14 <- readVcf("VCF_ERP011529_GRCm39/ERX1059314_svtyper.vcf", "GRCm39")
r06 <- rowRanges(v06)
r07 <- rowRanges(v07)
r08 <- rowRanges(v08)
r09 <- rowRanges(v09)
r10 <- rowRanges(v10)
r11 <- rowRanges(v11)
r12 <- rowRanges(v12)
r13 <- rowRanges(v13)
r14 <- rowRanges(v14)
g06 <- as.vector(geno(v06)$GT)
g07 <- as.vector(geno(v07)$GT)
g08 <- as.vector(geno(v08)$GT)
g09 <- as.vector(geno(v09)$GT)
g10 <- as.vector(geno(v10)$GT)
g11 <- as.vector(geno(v11)$GT)
g12 <- as.vector(geno(v12)$GT)
g13 <- as.vector(geno(v13)$GT)
g14 <- as.vector(geno(v14)$GT)Reorganising the data
df <- data.frame(rowRanges(v06),info(v06)) #taking a look into the content for one of the vcf file.
df <- df[,c("seqnames","start","END")]
head(df)## seqnames start END
## 1 1 4194031 4194125
## 2 1 7260451 7267086
## 3 1 9586809 9586912
## 4_1 1 10403838 NA
## 4_2 1 10404071 NA
## 5 1 12308508 12308613alt <- unlist(as.vector(elementMetadata(v06)$ALT))
svtype <- info(v06)$SVTYPE
# need to add g14
str(g14)## chr [1:9423] "0/1" "1/1" "0/0" "0/0" "0/0" "0/0" "./." "0/0" "0/0" "0/1" ...gt <- data.frame(g06,g07,g08,g09,g10,g11,g12,g13,g14)
colnames(gt) <- c("g06","g07","g08","g09","g10","g11","g12","g13","g14")
qual <- data.frame(r06$QUAL,r07$QUAL,r08$QUAL,r09$QUAL,r10$QUAL,r11$QUAL,r11$QUAL,r12$QUAL,r13$QUAL,r14$QUAL)
gt2 <- data.frame(df,alt,svtype,gt,qual)
head(gt2,20)## seqnames start END alt svtype g06 g07 g08 g09 g10 g11
## 1 1 4194031 4194125 <DEL> DEL 0/1 0/0 0/0 0/0 0/0 0/0
## 2 1 7260451 7267086 <DEL> DEL 1/1 1/1 1/1 1/1 1/1 1/1
## 3 1 9586809 9586912 <DEL> DEL 0/0 0/0 0/0 0/0 0/1 0/0
## 4_1 1 10403838 NA [1:10404071[N BND 0/0 0/0 0/0 0/0 0/0 0/0
## 4_2 1 10404071 NA [1:10403838[N BND 0/0 0/0 0/0 0/0 0/0 0/0
## 5 1 12308508 12308613 <DEL> DEL 0/0 0/0 0/0 0/0 0/0 0/1
## 6 1 13054313 13054414 <DEL> DEL ./. 0/0 0/0 1/1 ./. ./.
## 7_1 1 11722322 NA N]1:15057495] BND 0/0 0/1 0/0 0/0 0/0 0/0
## 7_2 1 15057495 NA N]1:11722322] BND 0/0 0/1 0/0 0/0 0/0 0/0
## 8 1 15371302 15371454 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1
## 9_1 1 12594703 NA [1:16313610[N BND 0/1 0/0 0/0 0/0 0/0 0/0
## 9_2 1 16313610 NA [1:12594703[N BND 0/1 0/0 0/0 0/0 0/0 0/0
## 10_1 1 17386992 NA N]1:17387262] BND 0/0 0/0 0/0 0/0 0/0 0/0
## 10_2 1 17387262 NA N]1:17386992] BND 0/0 0/0 0/0 0/0 0/0 0/0
## 11 1 10439801 19263164 <DEL> DEL 0/1 0/0 0/1 0/1 0/0 0/1
## 12 1 19985032 19985086 <DEL> DEL 0/0 0/0 0/0 0/0 0/0 0/0
## 13 1 3780995 20608149 <DUP> DUP 0/0 0/0 0/0 0/1 0/0 0/0
## 14 1 21246128 21246249 <DEL> DEL 0/0 0/0 0/0 0/1 0/0 0/1
## 15 1 22608937 22609054 <DEL> DEL 0/0 0/0 0/0 0/0 0/0 0/0
## 16 1 22935010 22935062 <DEL> DEL 0/0 0/0 1/1 ./. 0/0 0/0
## g12 g13 g14 r06.QUAL r07.QUAL r08.QUAL r09.QUAL r10.QUAL r11.QUAL
## 1 0/0 0/0 0/1 21.31 0.07 0.13 1.01 0.07 2.04
## 2 1/1 1/1 1/1 384.05 590.85 856.73 915.82 443.14 797.65
## 3 0/0 0/1 0/0 4.77 0.02 0.02 0.13 38.95 2.04
## 4_1 0/0 0/0 0/0 0.00 0.00 0.00 0.00 0.02 0.00
## 4_2 0/0 0/0 0/0 0.00 0.00 0.00 0.00 0.02 0.00
## 5 0/0 0/0 0/0 0.52 0.52 0.26 1.01 0.13 53.14
## 6 1/1 0/0 ./. 0.00 4.77 0.26 31.46 0.00 0.00
## 7_1 0/0 0/0 0/0 0.00 12.11 0.00 0.00 0.00 0.00
## 7_2 0/0 0/0 0/0 0.00 12.11 0.00 0.00 0.00 0.00
## 8 0/1 0/1 0/1 6.93 35.88 23.94 89.93 218.86 38.82
## 9_1 0/0 0/0 0/0 26.93 0.00 0.00 0.00 0.00 0.00
## 9_2 0/0 0/0 0/0 26.93 0.00 0.00 0.00 0.00 0.00
## 10_1 0/0 0/0 0/0 0.00 0.00 0.00 0.00 0.00 0.00
## 10_2 0/0 0/0 0/0 0.00 0.00 0.00 0.00 0.00 0.00
## 11 0/0 0/1 0/1 233.76 0.01 62.29 11.87 0.00 71.57
## 12 0/0 0/1 0/0 0.52 0.07 0.00 0.00 0.00 0.00
## 13 0/0 0/0 0/0 0.56 0.00 0.05 6.77 0.00 0.01
## 14 0/0 0/0 0/0 0.00 0.00 0.00 26.87 0.06 29.87
## 15 0/1 0/0 0/0 2.04 0.26 0.02 0.03 0.52 4.77
## 16 0/0 0/0 0/0 4.77 2.04 31.46 0.00 1.01 2.04
## r11.QUAL.1 r12.QUAL r13.QUAL r14.QUAL
## 1 2.04 0.00 0.00 25.33
## 2 797.65 945.36 945.36 797.65
## 3 2.04 2.04 9.47 0.26
## 4_1 0.00 0.00 0.00 0.00
## 4_2 0.00 0.00 0.00 0.00
## 5 53.14 0.01 4.77 0.13
## 6 0.00 31.46 4.77 0.00
## 7_1 0.00 0.00 0.00 0.00
## 7_2 0.00 0.00 0.00 0.00
## 8 38.82 161.81 350.74 449.68
## 9_1 0.00 0.00 0.00 0.00
## 9_2 0.00 0.00 0.00 0.00
## 10_1 0.00 0.00 0.00 0.00
## 10_2 0.00 0.00 0.00 0.00
## 11 71.57 0.00 122.48 17.48
## 12 0.00 0.00 20.76 0.00
## 13 0.01 0.00 0.00 0.00
## 14 29.87 0.00 0.00 0.00
## 15 4.77 9.47 0.00 0.13
## 16 2.04 4.77 4.77 1.01gt3 <- gt2[which(apply(qual,1,min)>=20),]
head(gt3,20)## seqnames start END alt svtype g06 g07 g08 g09 g10 g11 g12 g13
## 2 1 7260451 7267086 <DEL> DEL 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 24 1 26725045 26727518 <DUP> DUP 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 143 1 88161964 88161971 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 146 1 88198038 88199164 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 147 1 88199973 88200213 <DEL> DEL 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1
## 150 1 88220342 88222032 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 151 1 88225613 88225618 <DEL> DEL 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1
## 278 1 137906288 137906311 <DEL> DEL 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 305 1 145830816 145834233 <DUP> DUP 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 379 1 171172579 171184095 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 380 1 171172578 171185415 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 381 1 171184396 171185415 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 473 2 3050626 3050644 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 474 2 3050001 3051081 <DUP> DUP 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1
## 478 2 3050626 3051058 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 479 2 3050626 3050758 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 482 2 3050730 3051499 <DUP> DUP 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 483 2 3050132 3051543 <DUP> DUP 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 594 2 5384180 72843078 <DEL> DEL 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 656 2 98492844 98493120 <DUP> DUP 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1
## g14 r06.QUAL r07.QUAL r08.QUAL r09.QUAL r10.QUAL r11.QUAL r11.QUAL.1
## 2 1/1 384.05 590.85 856.73 915.82 443.14 797.65 797.65
## 24 1/1 681.41 1208.81 1743.76 1794.60 1990.40 1646.78 1646.78
## 143 0/1 545.61 317.80 581.62 428.78 890.47 524.70 524.70
## 146 0/1 749.38 1133.18 2008.43 1450.98 2902.16 1676.11 1676.11
## 147 0/1 1508.16 1454.18 4256.14 2752.86 5406.32 2378.61 2378.61
## 150 0/1 1799.10 2464.76 3750.99 2395.82 3178.39 2455.74 2455.74
## 151 1/1 320.81 551.69 1172.39 821.69 1652.13 1061.81 1061.81
## 278 1/1 31.46 89.31 89.31 60.25 31.46 118.56 118.56
## 305 1/1 150.74 421.40 479.55 320.15 377.31 389.67 389.67
## 379 0/1 272.26 23.81 797.16 443.22 1420.99 458.38 458.38
## 380 0/1 23.49 53.79 476.48 185.54 458.38 131.62 131.62
## 381 0/1 80.71 170.70 719.26 212.66 536.28 98.62 98.62
## 473 0/1 802.98 1261.80 926.03 1576.40 854.14 1264.36 1264.36
## 474 0/1 294.28 498.80 518.55 603.97 521.97 791.84 791.84
## 478 0/1 294.33 788.72 618.27 1691.08 1323.90 826.96 826.96
## 479 0/1 1112.91 1766.55 1104.09 2574.45 2075.52 1647.08 1647.08
## 482 0/1 106.20 508.43 374.73 415.12 142.18 284.47 284.47
## 483 1/1 182.31 474.39 512.98 735.36 658.63 871.74 871.74
## 594 0/1 3115.39 1916.01 659.39 1391.06 71.50 194.56 194.56
## 656 1/1 160236.04 184683.75 169964.87 138012.91 117231.55 151341.40 151341.40
## r12.QUAL r13.QUAL r14.QUAL
## 2 945.36 945.36 797.65
## 24 1640.37 2905.85 3045.66
## 143 374.79 830.54 788.59
## 146 992.16 1981.82 2467.64
## 147 1442.22 4551.08 4344.70
## 150 3544.16 4155.97 4080.95
## 151 839.56 1641.73 1572.83
## 278 118.56 236.38 177.38
## 305 466.85 653.25 597.49
## 379 194.68 800.23 1330.81
## 380 146.78 440.47 533.40
## 381 344.66 674.42 392.44
## 473 1477.08 1561.18 1627.06
## 474 709.13 957.42 789.10
## 478 1126.34 1726.19 1924.27
## 479 1873.10 1753.57 2404.39
## 482 323.39 293.39 81.36
## 483 797.76 1373.83 1651.61
## 594 284.61 221.61 371.52
## 656 154837.87 124181.71 125770.52gt <- gt[which(apply(qual,1,min)>=20),]
head(gt,20)## g06 g07 g08 g09 g10 g11 g12 g13 g14
## 2 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 32 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 184 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 187 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 188 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1
## 191 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 192 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1
## 375 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 416 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 513 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 514 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 515 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 643 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 644 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1
## 648 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 649 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 652 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 653 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1
## 794 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1
## 885 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1rd <- rowRanges(v06)
rd <- rd[which(apply(qual,1,min)>=20),]
head(rd,20)## GRanges object with 20 ranges and 5 metadata columns:
## seqnames ranges strand | paramRangeID REF ALT
## <Rle> <IRanges> <Rle> | <factor> <DNAStringSet> <CharacterList>
## 2 1 7260451 * | NA N <DEL>
## 24 1 26725045 * | NA N <DUP>
## 143 1 88161964 * | NA N <DEL>
## 146 1 88198038 * | NA N <DEL>
## 147 1 88199973 * | NA N <DEL>
## ... ... ... ... . ... ... ...
## 479 2 3050626 * | NA N <DEL>
## 482 2 3050730 * | NA N <DUP>
## 483 2 3050132 * | NA N <DUP>
## 594 2 5384180 * | NA N <DEL>
## 656 2 98492844 * | NA N <DUP>
## QUAL FILTER
## <numeric> <character>
## 2 384.05 .
## 24 681.41 .
## 143 545.61 .
## 146 749.38 .
## 147 1508.16 .
## ... ... ...
## 479 1112.91 .
## 482 106.20 .
## 483 182.31 .
## 594 3115.39 .
## 656 160236.04 .
## -------
## seqinfo: 26 sequences from GRCm39 genome; no seqlengthsrows <- which(apply(gt,1,function(x){
sd(as.numeric(as.factor(x)))
})!=0)
gt3 <- gt3[rows,]
gt <- gt[rows,]
gtx <- apply(gt,2,function(x) { as.numeric(as.factor(x))})
rownames(gtx) <- paste(gt3$seqnames,gt3$start,gt3$END,gt3$alt)
gtx## g06 g07 g08 g09 g10 g11 g12 g13 g14
## 1 88199973 88200213 <DEL> 1 1 2 2 1 2 1 2 1
## 1 88225613 88225618 <DEL> 1 2 1 1 1 2 1 2 2
## 2 3050001 3051081 <DUP> 1 1 1 1 2 1 1 1 1
## 2 98492844 98493120 <DUP> 2 2 2 2 2 1 1 2 2
## 2 98492585 NA [2:98493182[N 1 2 2 2 1 1 1 1 1
## 2 98493182 NA [2:98492585[N 1 2 2 2 1 1 1 1 1
## 2 177006296 177007038 <DUP> 1 1 1 1 1 1 1 1 2
## 3 3001937 3002231 <DUP> 2 2 1 2 2 1 1 2 2
## 3 3022412 3041367 <DUP> 1 1 1 1 2 1 1 2 2
## 3 3024954 3041361 <DUP> 1 2 1 1 2 2 1 2 2
## 3 3056508 3066796 <DUP> 2 2 2 2 1 1 2 1 1
## 3 3104653 3203067 <DUP> 2 1 2 2 2 1 1 1 1
## 3 3102714 3228384 <DUP> 2 2 2 2 2 1 2 2 2
## 3 3007433 56483169 <DUP> 2 2 2 1 1 1 1 1 1
## 3 79211043 79211222 <DEL> 2 1 2 2 1 2 1 1 1
## 3 106030378 106218721 <DUP> 2 2 1 2 2 2 2 2 2
## 4 3067784 3080999 <DUP> 1 1 1 1 2 2 2 2 2
## 4 3067729 3081005 <DUP> 1 1 1 1 1 2 2 2 2
## 4 3052971 3082223 <DUP> 1 2 2 2 2 2 1 2 2
## 4 3081729 3082613 <DUP> 1 2 1 2 2 2 1 2 2
## 4 3052971 3083879 <DUP> 1 1 2 2 2 2 2 2 2
## 4 3061975 3084488 <DUP> 1 1 1 1 2 2 2 2 2
## 4 21973643 34311904 <DEL> 2 1 1 2 1 2 1 1 1
## 4 145135113 145310160 <DUP> 2 2 1 1 2 1 1 2 2
## 4 145166301 147562193 <DUP> 1 2 2 2 2 2 2 2 2
## 4 145166301 147583939 <DUP> 1 2 1 2 2 2 2 2 2
## 4 145284285 147687379 <DUP> 2 1 1 2 1 2 2 2 2
## 4 147901236 147901302 <DEL> 1 1 1 2 1 1 1 1 2
## 4 156401048 NA [4:156401116[N 1 1 1 1 2 1 2 1 1
## 4 156401116 NA [4:156401048[N 1 1 1 1 2 1 2 1 1
## 5 77571649 77572420 <DEL> 1 1 1 1 1 1 1 1 2
## 5 148739439 148740254 <DUP> 1 1 2 1 2 2 2 2 2
## 6 115999365 116001761 <DEL> 1 1 2 2 2 2 1 1 2
## 7 11744767 11749209 <DEL> 1 2 1 1 1 1 1 1 1
## 7 11746752 11749431 <DEL> 1 1 1 1 1 1 1 1 2
## 7 11747360 11749831 <DUP> 1 1 1 1 2 1 2 1 1
## 7 23800993 23803828 <DEL> 2 1 1 1 1 1 1 1 1
## 7 7280874 25259664 <DUP> 2 2 2 2 2 2 1 2 1
## 9 3000001 3006955 <DUP> 1 1 1 1 2 1 1 2 2
## 9 3018984 3024669 <DUP> 1 1 1 1 2 1 1 1 2
## 9 3001934 3024667 <DUP> 1 1 1 1 2 1 1 2 2
## 9 3023344 3024702 <DUP> 1 1 1 1 2 1 1 1 1
## 9 3006638 3024677 <DUP> 1 1 1 1 2 1 1 2 2
## 9 3023362 3038236 <DUP> 2 2 2 1 1 1 1 1 1
## 9 56168047 56225946 <DEL> 2 1 2 2 2 1 1 2 2
## 9 103242388 103242439 <DEL> 1 1 2 2 2 1 2 2 1
## 10 21941921 NA N]10:72133193] 2 1 1 2 1 1 1 1 1
## 10 72133193 NA N]10:21941921] 2 1 1 2 1 1 1 1 1
## 11 66455435 66456139 <DUP> 1 1 2 2 2 2 2 2 2
## 11 88858545 88861862 <DUP> 1 1 1 2 2 2 1 2 2
## 12 114723381 114762156 <DUP> 2 2 2 2 2 1 2 2 2
## 13 51527238 51527533 <DUP> 1 2 2 1 1 1 1 1 1
## 14 3053318 3054003 <DUP> 2 2 2 1 1 1 1 1 1
## 15 69756413 69756834 <DUP> 2 1 2 2 2 2 2 2 1
## 16 3054417 3059463 <DUP> 1 1 2 1 2 1 1 1 2
## 16 37243917 37244040 <DEL> 1 1 1 1 1 1 1 2 1
## 16 97811706 97812744 <DUP> 1 1 1 2 1 1 1 2 1
## 17 3061396 3062427 <DUP> 1 2 2 1 2 2 2 2 2
## 17 3072667 3084145 <DUP> 1 2 2 1 2 1 2 2 1
## 17 13810163 13811871 <DUP> 1 1 2 1 2 2 2 2 2
## 17 13874874 13875560 <DUP> 1 1 1 1 2 2 2 2 2
## 17 13810165 13875559 <DUP> 1 1 1 1 1 1 1 2 1
## 17 23652034 23652196 <DEL> 1 1 1 1 1 2 1 2 2
## 17 23734345 23735340 <DEL> 2 1 1 1 1 1 1 1 1
## X 30843614 NA N]X:33301901] 2 1 1 1 1 1 1 1 1
## X 33301901 NA N]X:30843614] 2 1 1 1 1 1 1 1 1
## X 51974565 51975592 <DUP> 2 2 2 2 1 2 1 2 2
## X 75642155 75642714 <DUP> 1 1 2 1 2 1 1 2 2
## Y 4021770 4021972 <DEL> 2 2 2 2 1 1 1 2 1
## Y 90751285 90751458 <DEL> 1 1 1 1 1 1 1 2 1
## Y 90751648 90751679 <DEL> 1 1 1 1 1 1 1 2 1
## Y 90736508 90820037 <DEL> 1 1 1 1 1 1 1 2 1
## Y 90731064 90820037 <DEL> 1 1 1 1 1 1 1 2 1
## Y 90736331 90820037 <DEL> 1 1 1 1 1 1 1 2 1
## Y 90733670 90820037 <DEL> 1 1 1 1 1 1 1 2 1
## Y 90817330 90820433 <DUP> 1 1 1 1 1 1 1 2 1
## Y 90728744 90820433 <DUP> 2 2 2 2 1 1 1 2 1
## Y 90824763 90825061 <DEL> 2 2 2 1 2 2 1 2 1
## MT 81 16299 <DUP> 1 2 1 1 1 1 1 1 1rd <- rd[rows,]
rd## GRanges object with 79 ranges and 5 metadata columns:
## seqnames ranges strand | paramRangeID REF ALT
## <Rle> <IRanges> <Rle> | <factor> <DNAStringSet> <CharacterList>
## 147 1 88199973 * | NA N <DEL>
## 151 1 88225613 * | NA N <DEL>
## 474 2 3050001 * | NA N <DUP>
## 656 2 98492844 * | NA N <DUP>
## 669_1 2 98492585 * | NA N [2:98493182[N
## ... ... ... ... . ... ... ...
## 6488 Y 90733670 * | NA N <DEL>
## 6489 Y 90817330 * | NA N <DUP>
## 6490 Y 90728744 * | NA N <DUP>
## 6503 Y 90824763 * | NA N <DEL>
## 7402 MT 81 * | NA N <DUP>
## QUAL FILTER
## <numeric> <character>
## 147 1508.16 .
## 151 320.81 .
## 474 294.28 .
## 656 160236.04 .
## 669_1 1399.47 .
## ... ... ...
## 6488 2907.41 .
## 6489 364.97 .
## 6490 779.91 .
## 6503 1229.02 .
## 7402 46210.09 .
## -------
## seqinfo: 26 sequences from GRCm39 genome; no seqlengthscolfunc <- colorRampPalette(c("blue", "red"))
library(gplots)## Registered S3 method overwritten by 'gplots':
## method from
## plot.venn eulerr##
## Attaching package: 'gplots'## The following object is masked from 'package:eulerr':
##
## venn## The following object is masked from 'package:IRanges':
##
## space## The following object is masked from 'package:S4Vectors':
##
## space## The following object is masked from 'package:stats':
##
## lowessheatmap.2(gtx, trace = "none", scale = "none",
dendrogram='none', Rowv=FALSE, Colv=FALSE, col=colfunc(25),
margins = c(5,20), cexRow=.8, cexCol=.9, main="Genetic Variation")
Session Information
sessionInfo()## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] gplots_3.1.1 VariantAnnotation_1.38.0
## [3] Rsamtools_2.8.0 SummarizedExperiment_1.22.0
## [5] Biobase_2.52.0 MatrixGenerics_1.4.3
## [7] matrixStats_0.60.1 eulerr_6.1.1
## [9] Biostrings_2.60.2 XVector_0.32.0
## [11] R.utils_2.10.1 R.oo_1.24.0
## [13] R.methodsS3_1.8.1 GenomicRanges_1.44.0
## [15] GenomeInfoDb_1.28.4 IRanges_2.26.0
## [17] S4Vectors_0.30.0 BiocGenerics_0.38.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.2 sass_0.4.0 bit64_4.0.5
## [4] jsonlite_1.7.2 gtools_3.9.2 bslib_0.3.0
## [7] assertthat_0.2.1 highr_0.9 BiocFileCache_2.0.0
## [10] blob_1.2.2 BSgenome_1.60.0 GenomeInfoDbData_1.2.6
## [13] yaml_2.2.1 progress_1.2.2 pillar_1.6.2
## [16] RSQLite_2.2.8 lattice_0.20-44 glue_1.4.2
## [19] digest_0.6.27 htmltools_0.5.2 Matrix_1.3-4
## [22] XML_3.99-0.7 pkgconfig_2.0.3 biomaRt_2.48.3
## [25] zlibbioc_1.38.0 purrr_0.3.4 BiocParallel_1.26.2
## [28] tibble_3.1.4 KEGGREST_1.32.0 generics_0.1.0
## [31] ellipsis_0.3.2 cachem_1.0.6 GenomicFeatures_1.44.2
## [34] magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0
## [37] evaluate_0.14 fansi_0.5.0 xml2_1.3.2
## [40] tools_4.1.1 prettyunits_1.1.1 hms_1.1.0
## [43] BiocIO_1.2.0 lifecycle_1.0.0 stringr_1.4.0
## [46] DelayedArray_0.18.0 AnnotationDbi_1.54.1 compiler_4.1.1
## [49] jquerylib_0.1.4 caTools_1.18.2 rlang_0.4.11
## [52] grid_4.1.1 RCurl_1.98-1.4 rjson_0.2.20
## [55] rappdirs_0.3.3 bitops_1.0-7 rmarkdown_2.11
## [58] restfulr_0.0.13 curl_4.3.2 DBI_1.1.1
## [61] R6_2.5.1 GenomicAlignments_1.28.0 rtracklayer_1.52.1
## [64] knitr_1.34 dplyr_1.0.7 fastmap_1.1.0
## [67] bit_4.0.4 utf8_1.2.2 filelock_1.0.2
## [70] KernSmooth_2.23-20 stringi_1.7.4 Rcpp_1.0.7
## [73] vctrs_0.3.8 png_0.1-7 dbplyr_2.1.1
## [76] tidyselect_1.1.1 xfun_0.26