VCF files can contain vast quantities of data, from many chromosomes. However, in cases where only the data from specific genes or genomic regions are required for analysis, these regions can be extracted in R using the Bioconductor GenomicRanges package in R.
IRanges is a library for representing integer ranges, which is useful in genomics because we need to manipulate base pair ranges.
IRanges have a start, an end and an witdh.
Set working directory:
setwd = ("C:/Users/manso/OneDrive - University of West London/MSc Bioinformatics - UWL/3.DSB - Data Science for Bioinformatics/Practice/W13 - Genomic Intervals and Genome Arithmetic")
Install packages:
install.packages("BiocManager")
BiocManager::install(c("GenomicRanges", "plyranges", "HelloRangesData"))
#IR with 6 base-apirs long: start and end are indicated
IR <- IRanges(5,10)
IR
IRanges object with 1 range and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 5 10 6start(IR) #return the start value
[1] 5end(IR) #return
[1] 10width(IR) #return the width
[1] 6library(plyranges, quietly = TRUE)
genes <- data.frame(seqnames = "VI",
start = c(3322, 3030, 1437, 5066, 6426, 836),
end = c(3846, 3338, 2615, 5521, 7565, 1363),
strand = c("-", "-", "-", "+", "+", "+"),
gene_id=c("YFL064C", "YFL065C", "YFL066C",
"YFL063W", "YFL062W", "YFL067W"),
gc = runif(6),
score = rbinom(6, size = 3, p = 0.1),
stringsAsFactors = FALSE)
genes <- as_granges(genes)
genes
GRanges object with 6 ranges and 3 metadata columns:
seqnames ranges strand | gene_id gc score
<Rle> <IRanges> <Rle> | <character> <numeric> <integer>
[1] VI 3322-3846 - | YFL064C 0.77730361 0
[2] VI 3030-3338 - | YFL065C 0.00456595 0
[3] VI 1437-2615 - | YFL066C 0.57144666 1
[4] VI 5066-5521 + | YFL063W 0.30042006 0
[5] VI 6426-7565 + | YFL062W 0.65073446 1
[6] VI 836-1363 + | YFL067W 0.53914336 0
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengthsrng <- as_iranges(data.frame(start=c(1,2,3), end=c(5,2,8)))
grng <- as_granges(data.frame(start=c(1,2,3), end=c(5,2,8),
seqnames = "seq1",
strand=c("+", "*", "-")))
grng
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] seq1 1-5 +
[2] seq1 2 *
[3] seq1 3-8 -
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengthsmutate(rng, width =10)
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 10 10
[2] 2 11 10
[3] 3 12 10Anchoring fixes either the start, end, center coordinates of the range object, as shown in the figure and code below. Anchors are used in combination with either mutate od stretch.
mutate(anchor_start(rng), width=10)
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 10 10
[2] 2 11 10
[3] 3 12 10mutate(anchor_end(rng), width=10)
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] -4 5 10
[2] -7 2 10
[3] -1 8 10mutate(anchor_center(rng), width=10)
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] -2 7 10
[2] -3 6 10
[3] 1 10 10rng
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6if (!requireNamespace("BiocManager", quietly =TRUE))
install.packages("BiocManager")
BiocManager::install("Rsamtools")
BiocManager::install("biomaRt")
BiocManager::install("VariantAnnotation")
VCFChr7 <-
TabixFile("ALL.chr7.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz")
ensembl <- useMart("ensembl")
datasets <- listDatasets(ensembl)
ensembl = useDataset("hsapiens_gene_ensembl", mart=ensembl)
hg38 <- ensembl
seqnames(VCFAOC1)
factor-Rle of length 1063 with 1 run
Lengths: 1063
Values : 7
Levels(86): 1 2 3 4 5 6 7 ... GL000249.1 MT NC_007605 X Y hs37d5ranges(VCFAOC1)
IRanges object with 1063 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
7:150824913_G/A 150824913 150824913 1
7:150825001_C/G 150825001 150825001 1
7:150825031_C/T 150825031 150825031 1
7:150825032_G/A 150825032 150825032 1
7:150825037_T/C 150825037 150825037 1
... ... ... ...
7:150861125_C/A 150861125 150861125 1
7:150861130_T/TA 150861130 150861130 1
7:150861227_G/A 150861227 150861227 1
7:150861287_A/G 150861287 150861287 1
7:150861381_G/A 150861381 150861381 1strand(VCFAOC1)
factor-Rle of length 1063 with 1 run
Lengths: 1063
Values : *
Levels(3): + - *granges(VCFAOC1)
GRanges object with 1063 ranges and 5 metadata columns:
seqnames ranges strand | paramRangeID
<Rle> <IRanges> <Rle> | <factor>
7:150824913_G/A 7 150824913 * | AOC1
7:150825001_C/G 7 150825001 * | AOC1
7:150825031_C/T 7 150825031 * | AOC1
7:150825032_G/A 7 150825032 * | AOC1
7:150825037_T/C 7 150825037 * | AOC1
... ... ... ... . ...
7:150861125_C/A 7 150861125 * | AOC1
7:150861130_T/TA 7 150861130 * | AOC1
7:150861227_G/A 7 150861227 * | AOC1
7:150861287_A/G 7 150861287 * | AOC1
7:150861381_G/A 7 150861381 * | AOC1
REF ALT QUAL
<DNAStringSet> <DNAStringSetList> <numeric>
7:150824913_G/A G A 100
7:150825001_C/G C G 100
7:150825031_C/T C T 100
7:150825032_G/A G A 100
7:150825037_T/C T C 100
... ... ... ...
7:150861125_C/A C A 100
7:150861130_T/TA T TA 100
7:150861227_G/A G A 100
7:150861287_A/G A G 100
7:150861381_G/A G A 100
FILTER
<character>
7:150824913_G/A PASS
7:150825001_C/G PASS
7:150825031_C/T PASS
7:150825032_G/A PASS
7:150825037_T/C PASS
... ...
7:150861125_C/A PASS
7:150861130_T/TA PASS
7:150861227_G/A PASS
7:150861287_A/G PASS
7:150861381_G/A PASS
-------
seqinfo: 86 sequences from hg38 genomemcols(VCFAOC1)
DataFrame with 1063 rows and 5 columns
paramRangeID REF ALT
<factor> <DNAStringSet> <DNAStringSetList>
7:150824913_G/A AOC1 G A
7:150825001_C/G AOC1 C G
7:150825031_C/T AOC1 C T
7:150825032_G/A AOC1 G A
7:150825037_T/C AOC1 T C
... ... ... ...
7:150861125_C/A AOC1 C A
7:150861130_T/TA AOC1 T TA
7:150861227_G/A AOC1 G A
7:150861287_A/G AOC1 A G
7:150861381_G/A AOC1 G A
QUAL FILTER
<numeric> <character>
7:150824913_G/A 100 PASS
7:150825001_C/G 100 PASS
7:150825031_C/T 100 PASS
7:150825032_G/A 100 PASS
7:150825037_T/C 100 PASS
... ... ...
7:150861125_C/A 100 PASS
7:150861130_T/TA 100 PASS
7:150861227_G/A 100 PASS
7:150861287_A/G 100 PASS
7:150861381_G/A 100 PASSseqlengths(VCFAOC1)
1 2 3 4 5 6
249250621 243199373 198022430 191154276 180915260 171115067
7 8 9 10 11 12
159138663 146364022 141213431 135534747 135006516 133851895
13 14 15 16 17 18
115169878 107349540 102531392 90354753 81195210 78077248
19 20 21 22 GL000191.1 GL000192.1
59128983 63025520 48129895 51304566 106433 547496
GL000193.1 GL000194.1 GL000195.1 GL000196.1 GL000197.1 GL000198.1
189789 191469 182896 38914 37175 90085
GL000199.1 GL000200.1 GL000201.1 GL000202.1 GL000203.1 GL000204.1
169874 187035 36148 40103 37498 81310
GL000205.1 GL000206.1 GL000207.1 GL000208.1 GL000209.1 GL000210.1
174588 41001 4262 92689 159169 27682
GL000211.1 GL000212.1 GL000213.1 GL000214.1 GL000215.1 GL000216.1
166566 186858 164239 137718 172545 172294
GL000217.1 GL000218.1 GL000219.1 GL000220.1 GL000221.1 GL000222.1
172149 161147 179198 161802 155397 186861
GL000223.1 GL000224.1 GL000225.1 GL000226.1 GL000227.1 GL000228.1
180455 179693 211173 15008 128374 129120
GL000229.1 GL000230.1 GL000231.1 GL000232.1 GL000233.1 GL000234.1
19913 43691 27386 40652 45941 40531
GL000235.1 GL000236.1 GL000237.1 GL000238.1 GL000239.1 GL000240.1
34474 41934 45867 39939 33824 41933
GL000241.1 GL000242.1 GL000243.1 GL000244.1 GL000245.1 GL000246.1
42152 43523 43341 39929 36651 38154
GL000247.1 GL000248.1 GL000249.1 MT NC_007605 X
36422 39786 38502 16569 171823 155270560
Y hs37d5
59373566 35477943 names(VCFAOC1)
[1] "7:150824913_G/A" "7:150825001_C/G"
[3] "7:150825031_C/T" "7:150825032_G/A"
[5] "7:150825037_T/C" "7:150825060_C/T"
[7] "7:150825087_G/A" "7:150825096_G/C"
[9] "7:150825177_T/G" "7:150825201_G/T"
[11] "7:150825223_G/A" "7:150825315_G/A"
[13] "7:150825350_T/C" "7:150825389_C/T"
[15] "7:150825394_T/A" "7:150825420_C/T"
[17] "7:150825432_G/A" "7:150825492_A/G"
[19] "7:150825512_C/T" "7:150825567_C/T"
[21] "7:150825568_G/C" "7:150825574_G/C"
[23] "7:150825589_C/T" "7:150825593_C/T"
[25] "7:150825594_G/A" "7:150825629_G/A"
[27] "7:150825664_C/T" "7:150825675_G/A"
[29] "7:150825676_C/T" "7:150825688_G/A"
[31] "7:150825729_G/T" "7:150825806_T/A"
[33] "7:150825813_G/C" "7:150825839_G/A"
[35] "7:150825865_C/T" "7:150825866_G/A"
[37] "7:150825933_G/T" "7:150825939_C/G"
[39] "7:150825969_T/G" "7:150825981_A/G"
[41] "7:150825992_C/T" "7:150826035_A/C"
[43] "7:150826044_G/A" "7:150826207_G/A"
[45] "7:150826219_C/G" "7:150826313_C/T"
[47] "7:150826318_C/T" "7:150826345_C/T"
[49] "7:150826385_A/G" "7:150826406_C/G"
[51] "7:150826415_G/A" "7:150826423_C/T"
[53] "7:150826434_GC/G" "7:150826443_C/T"
[55] "7:150826454_G/A" "7:150826470_C/T"
[57] "7:150826471_G/A" "7:150826500_G/C"
[59] "7:150826545_C/G" "7:150826555_A/G"
[61] "7:150826561_C/T" "7:150826575_C/T"
[63] "7:150826623_C/G" "7:150826670_G/A"
[65] "7:150826673_C/T" "7:150826684_A/G"
[67] "7:150826687_C/T" "7:150826766_A/G"
[69] "7:150826818_CTCGCGAG/C" "7:150826912_G/A"
[71] "7:150826939_G/A" "7:150826950_C/A"
[73] "7:150826997_C/T" "7:150827104_G/A"
[75] "7:150827114_G/A" "7:150827117_C/T"
[77] "7:150827137_G/A" "7:150827175_G/A"
[79] "7:150827207_A/G" "7:150827235_C/T"
[81] "7:150827243_C/A" "7:150827245_C/T"
[83] "7:150827333_G/A" "7:150827336_G/A"
[85] "7:150827391_G/T" "7:150827478_C/T"
[87] "7:150827674_C/T" "7:150827682_G/A"
[89] "7:150827694_C/T" "7:150827695_G/A"
[91] "7:150827781_G/A" "7:150827794_C/CTA"
[93] "7:150827802_G/A" "7:150827860_C/T"
[95] "7:150827913_G/A" "7:150827933_G/A"
[97] "7:150827951_C/T" "7:150827975_T/C"
[99] "7:150828058_T/A" "7:150828059_T/C"
[101] "7:150828060_C/T" "7:150828122_G/C"
[103] "7:150828169_G/A" "7:150828219_C/T"
[105] "7:150828234_C/T" "7:150828249_C/T"
[107] "7:150828271_C/T" "7:150828275_C/G"
[109] "7:150828316_A/G" "7:150828344_A/C"
[111] "7:150828467_T/C" "7:150828468_A/G"
[113] "7:150828472_C/T" "7:150828530_G/C"
[115] "7:150828556_G/C" "7:150828564_T/C"
[117] "7:150828581_A/G" "7:150828609_C/T"
[119] "7:150828646_C/T" "7:150828673_C/T"
[121] "7:150828676_T/C" "7:150828692_G/C"
[123] "7:150828707_G/A" "7:150828713_G/A"
[125] "7:150828742_C/T" "7:150828789_G/A"
[127] "7:150828815_G/A" "7:150828858_G/A"
[129] "7:150828876_A/G" "7:150828988_C/A"
[131] "7:150829071_T/C" "7:150829082_G/A"
[133] "7:150829091_C/T" "7:150829101_G/T"
[135] "7:150829104_C/T" "7:150829197_C/T"
[137] "7:150829221_G/C" "7:150829222_G/A"
[139] "7:150829248_C/T" "7:150829263_A/G"
[141] "7:150829348_G/A" "7:150829351_C/T"
[143] "7:150829352_G/A" "7:150829378_G/A"
[145] "7:150829458_A/G" "7:150829475_C/G"
[147] "7:150829494_G/A" "7:150829511_T/C"
[149] "7:150829533_G/A" "7:150829613_C/T"
[151] "7:150829636_G/A" "7:150829657_A/G"
[153] "7:150829682_G/A" "7:150829684_A/G"
[155] "7:150829689_C/T" "7:150829709_G/A"
[157] "7:150829727_G/A" "7:150829728_C/T"
[159] "7:150829729_G/A" "7:150829736_T/C"
[161] "7:150829738_C/A" "7:150829743_C/A"
[163] "7:150829810_C/T" "7:150829828_G/A"
[165] "7:150829841_G/A" "7:150829936_C/T"
[167] "7:150829963_C/T" "7:150829978_C/T"
[169] "7:150830010_G/C" "7:150830015_A/G"
[171] "7:150830021_C/T" "7:150830033_C/T"
[173] "7:150830034_G/A" "7:150830037_G/A"
[175] "7:150830102_G/A" "7:150830109_T/A"
[177] "7:150830124_C/T" "7:150830126_C/A"
[179] "7:150830127_G/A" "7:150830148_G/A"
[181] "7:150830151_C/T" "7:150830221_A/G"
[183] "7:150830291_A/C" "7:150830341_G/A"
[185] "7:150830363_G/T" "7:150830385_C/T"
[187] "7:150830475_G/A" "7:150830505_G/A"
[189] "7:150830538_C/T" "7:150830548_C/T"
[191] "7:150830563_G/A" "7:150830593_C/T"
[193] "7:150830594_G/A" "7:150830624_C/T"
[195] "7:150830760_C/G" "7:150830806_C/T"
[197] "7:150830807_G/T" "7:150830866_C/T"
[199] "7:150830888_C/T" "7:150830889_G/A"
[201] "7:150830904_C/T" "7:150830956_C/T"
[203] "7:150830999_G/A" "7:150831032_G/A"
[205] "7:150831053_G/T" "7:150831098_G/C"
[207] "7:150831100_C/A" "7:150831101_A/G"
[209] "7:150831113_G/A" "7:150831205_C/T"
[211] "7:150831222_T/C" "7:150831229_C/T"
[213] "7:150831233_G/A" "7:150831254_C/T"
[215] "7:150831289_C/T" "7:150831309_C/T"
[217] "7:150831310_G/A" "7:150831315_G/A"
[219] "7:150831318_C/T" "7:150831319_G/A"
[221] "7:150831343_A/G" "7:150831363_G/A"
[223] "7:150831395_C/T" "7:150831430_A/G"
[225] "7:150831431_C/T" "7:150831477_C/T"
[227] "7:150831530_G/A" "7:150831602_G/A"
[229] "7:150831609_C/T" "7:150831626_G/A"
[231] "7:150831640_C/T" "7:150831662_C/T"
[233] "7:150831764_G/A" "7:150831772_C/T"
[235] "7:150831796_C/T" "7:150831808_C/T"
[237] "7:150831880_G/T" "7:150831915_G/A"
[239] "7:150831923_G/A" "7:150831953_C/T"
[241] "7:150831987_C/T" "7:150831988_G/A"
[243] "7:150832016_G/A" "7:150832022_G/A"
[245] "7:150832037_C/T" "7:150832051_G/A"
[247] "7:150832052_T/C" "7:150832073_G/A"
[249] "7:150832088_C/T" "7:150832110_T/G"
[251] "7:150832160_G/A" "7:150832217_A/T"
[253] "7:150832230_C/T" "7:150832265_A/G"
[255] "7:150832285_C/G" "7:150832327_G/A"
[257] "7:150832374_A/G" "7:150832381_C/T"
[259] "7:150832497_G/A" "7:150832512_A/G"
[261] "7:150832559_C/T" "7:150832616_A/G"
[263] "7:150832783_CA/C" "7:150832786_G/A"
[265] "7:150832913_A/G" "7:150832923_A/G"
[267] "7:150832959_A/G" "7:150832968_CCTAA/C"
[269] "7:150832993_A/C" "7:150832999_C/T"
[271] "7:150833040_A/G" "7:150833046_A/T"
[273] "7:150833130_C/T" "7:150833151_T/C"
[275] "7:150833170_T/G" "7:150833204_C/T"
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[279] "7:150833223_G/A" "7:150833270_C/G"
[281] "7:150833326_G/A" "7:150833333_G/A"
[283] "7:150833336_C/T" "7:150833343_C/A"
[285] "7:150833359_C/T" "7:150833380_C/T"
[287] "7:150833381_G/A" "7:150833438_C/T"
[289] "7:150833443_C/T" "7:150833467_C/A"
[291] "7:150833471_C/T" "7:150833504_G/A"
[293] "7:150833505_C/T" "7:150833517_G/A"
[295] "7:150833527_G/A" "7:150833563_C/T"
[297] "7:150833577_G/A" "7:150833579_T/C"
[299] "7:150833599_T/G" "7:150833620_C/T"
[301] "7:150833621_G/A" "7:150833625_C/T"
[303] "7:150833699_G/A" "7:150833755_CAAAG/C"
[305] "7:150833798_C/T" "7:150833799_G/A"
[307] "7:150833895_G/C" "7:150833940_A/G"
[309] "7:150834049_C/T" "7:150834088_C/G"
[311] "7:150834096_G/A" "7:150834114_G/T"
[313] "7:150834138_A/T" "7:150834166_G/A"
[315] "7:150834265_C/T" "7:150834306_C/T"
[317] "7:150834326_T/C" "7:150834348_C/T"
[319] "7:150834408_G/T" "7:150834428_GC/G"
[321] "7:150834434_G/A" "7:150834447_G/A"
[323] "7:150834488_G/C" "7:150834516_G/A"
[325] "7:150834539_C/T" "7:150834582_A/C"
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[891] "7:150854410_C/T" "7:150854442_T/C"
[893] "7:150854456_C/T" "7:150854478_AG/A"
[895] "7:150854501_C/T" "7:150854506_T/C"
[897] "7:150854510_C/A" "7:150854539_C/G"
[899] "7:150854629_G/T" "7:150854637_T/C"
[901] "7:150854647_C/A" "7:150854696_G/A"
[903] "7:150854713_G/A" "7:150854733_G/C"
[905] "7:150854751_C/T" "7:150854773_G/A"
[907] "7:150854778_CT/C" "7:150854796_C/T"
[909] "7:150854902_C/T" "7:150854926_G/A"
[911] "7:150854970_G/A" "7:150855025_C/T"
[913] "7:150855033_T/C" "7:150855133_A/G"
[915] "7:150855163_T/C" "7:150855169_TACAAG/T"
[917] "7:150855190_G/A" "7:150855232_A/G"
[919] "7:150855244_G/A" "7:150855311_C/T"
[921] "7:150855523_A/G" "7:150855532_TTTTTTG/T"
[923] "7:150855545_T/C" "7:150855550_G/T"
[925] "7:150855556_T/G" "7:150855583_G/A"
[927] "7:150855661_C/T" "7:150855662_G/A"
[929] "7:150855706_T/C" "7:150855745_G/A"
[931] "7:150855793_A/G" "7:150855801_T/C"
[933] "7:150855811_T/C" "7:150855950_G/A"
[935] "7:150855952_A/G" "7:150856045_T/A"
[937] "7:150856068_C/T" "7:150856115_C/T"
[939] "7:150856131_C/T" "7:150856147_C/G"
[941] "7:150856162_AAGT/A" "7:150856165_T/C"
[943] "7:150856172_A/T" "7:150856208_G/A"
[945] "7:150856226_T/C" "7:150856232_C/G"
[947] "7:150856268_C/T" "7:150856357_G/A"
[949] "7:150856390_C/T" "7:150856392_C/G"
[951] "7:150856393_G/A" "7:150856458_GA/G"
[953] "7:150856470_G/A" "7:150856476_G/A"
[955] "7:150856567_A/C" "7:150856592_C/T"
[957] "7:150856620_C/T" "7:150856654_A/G"
[959] "7:150856764_G/A" "7:150856780_G/A"
[961] "7:150856942_C/A" "7:150856966_A/G"
[963] "7:150857001_G/A" "7:150857128_G/C"
[965] "7:150857144_C/G" "7:150857176_G/T"
[967] "7:150857295_T/G" "7:150857346_C/T"
[969] "7:150857371_C/T" "7:150857465_C/T"
[971] "7:150857486_A/G" "7:150857556_G/A"
[973] "7:150857562_T/G" "7:150857632_C/A"
[975] "7:150857730_T/G" "7:150857746_T/G"
[977] "7:150857771_A/G" "7:150857798_C/T"
[979] "7:150857812_C/G" "7:150857824_C/A"
[981] "7:150857876_A/C" "7:150857906_C/T"
[983] "7:150857907_G/A" "7:150857956_A/C"
[985] "7:150857960_C/T" "7:150857963_T/G"
[987] "7:150857975_T/C" "7:150857978_G/C"
[989] "7:150857983_T/C" "7:150857998_C/T"
[991] "7:150858180_T/C" "7:150858192_C/G"
[993] "7:150858194_G/A" "7:150858209_A/G"
[995] "7:150858271_A/G" "7:150858337_T/C"
[997] "7:150858347_T/C" "7:150858349_C/A"
[999] "7:150858354_A/G" "7:150858459_T/C"
[1001] "7:150858514_G/T" "7:150858541_AGGG/A"
[1003] "7:150858602_A/G" "7:150858616_T/C"
[1005] "7:150858657_G/A" "7:150858660_G/A"
[1007] "7:150858688_C/G" "7:150858731_G/A"
[1009] "7:150858801_G/A" "7:150859031_G/C"
[1011] "7:150859179_C/G" "7:150859180_T/G"
[1013] "7:150859211_G/A" "7:150859264_G/A"
[1015] "7:150859315_C/A" "7:150859358_C/A"
[1017] "7:150859361_G/A" "7:150859381_T/C"
[1019] "7:150859384_C/T" "7:150859468_G/C"
[1021] "7:150859492_G/A" "7:150859521_A/T"
[1023] "7:150859533_C/T" "7:150859597_A/G"
[1025] "7:150859598_A/G" "7:150859748_A/G"
[1027] "7:150859838_T/C" "7:150859891_CT/C"
[1029] "7:150860036_G/A" "7:150860055_G/A"
[1031] "7:150860067_A/T" "7:150860098_G/T"
[1033] "7:150860144_C/T" "7:150860153_A/G"
[1035] "7:150860182_C/T" "7:150860183_G/A"
[1037] "7:150860201_T/G" "7:150860246_G/A"
[1039] "7:150860330_G/A" "7:150860353_C/T"
[1041] "7:150860383_C/T" "7:150860448_C/T"
[1043] "7:150860528_G/A" "7:150860541_C/T"
[1045] "7:150860621_A/G" "7:150860657_T/C"
[1047] "7:150860677_A/C" "7:150860739_T/A"
[1049] "7:150860772_C/T" "7:150860846_T/C"
[1051] "7:150860889_C/T" "7:150860890_T/C"
[1053] "7:150860993_C/T" "7:150861060_C/A"
[1055] "7:150861061_A/G" "7:150861070_T/G"
[1057] "7:150861081_C/T" "7:150861098_G/C"
[1059] "7:150861125_C/A" "7:150861130_T/TA"
[1061] "7:150861227_G/A" "7:150861287_A/G"
[1063] "7:150861381_G/A" length(VCFAOC1)
[1] 1063