parse_vcf: Parse a VCF file
In jhrcook/KrasAlleleCna: The Allele-Specific CNA Analysis of KRAS in CRC
Description
Usage
Arguments
Value
Examples
Description
Parse the read-depth information of a VCF file produced by
mpileup
Usage
1
parse_vcf(fname)
Arguments
fname
path to the file
Value
a tibble
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
## Not run:
# head of the VCF file
#> ##fileformat=VCFv4.2
#> ##FILTER=<ID=PASS,Description="All filters passed">
#> ##bcftoolsVersion=1.9+htslib-1.9
#> ##bcftoolsCommand=mpileup -Ov --annotate INFO/AD,FORMAT/AD,FORMAT/DP ...
#> ##reference=file:///n/no_backup2/dbmi/park/jc604/databases/reference_...
#> ##contig=<ID=chr1,length=248956422>
#> ##contig=<ID=chr2,length=242193529>
#> ##contig=<ID=chr3,length=198295559>
#> ##contig=<ID=chr4,length=190214555>
#> ##contig=<ID=chr5,length=181538259>
#> ##contig=<ID=chr6,length=170805979>
#> ##contig=<ID=chr7,length=159345973>
#> ##contig=<ID=chr8,length=145138636>
#> ##contig=<ID=chr9,length=138394717>
#> ##contig=<ID=chr10,length=133797422>
#> ##contig=<ID=chr11,length=135086622>
#> ##contig=<ID=chr12,length=133275309>
#> ##contig=<ID=chr13,length=114364328>
#> ##contig=<ID=chr14,length=107043718>
#> ##contig=<ID=chr15,length=101991189>
#> ##contig=<ID=chr16,length=90338345>
#> ##contig=<ID=chr17,length=83257441>
#> ##contig=<ID=chr18,length=80373285>
#> ##contig=<ID=chr19,length=58617616>
#> ##contig=<ID=chr20,length=64444167>
#> ##contig=<ID=chr21,length=46709983>
#> ##contig=<ID=chr22,length=50818468>
#> ##contig=<ID=chrX,length=156040895>
#> ##contig=<ID=chrY,length=57227415>
#> ##contig=<ID=chrM,length=16569>
#> ##contig=<ID=chr1_KI270706v1_random,length=175055>
#> ##contig=<ID=chr1_KI270707v1_random,length=32032>
#> ##contig=<ID=chr1_KI270708v1_random,length=127682>
#> ...
#> ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
#> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
#> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
#> ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic depths">
#> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TCGA-FZ-5924-01A-13D-1609-08
#> chr12 25202434 . A <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,29,841,0,0,60,3600,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,29:1:1,0
#> chr12 25202435 . G <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,31,961,0,0,60,3600,0,0,1,1,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,31:1:1,0
#> chr12 25202436 . C <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,28,784,0,0,60,3600,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,28:1:1,0
#> chr12 25202437 . A <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,30,900,0,0,60,3600,0,0,3,9,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,30:1:1,0
#> chr12 25202438 . G <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,4,16,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,34:1:1,0
#> chr12 25202439 . G <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,5,25,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,33:1:1,0
#> ...
parse_vcf("example.vcf")
#> # A tibble: 8,917 x 7
#> start ref alt qual read_info num_high_qual_bas<e2><80><a6> allelic_depths
#> <dbl> <chr> <chr> <dbl> <chr> <chr> <chr>
#> 1 25202434 A <*> 0 0,3,29:1:1,0 1 1
#> 2 25202435 G <*> 0 0,3,31:1:1,0 1 1
#> 3 25202436 C <*> 0 0,3,28:1:1,0 1 1
#> 4 25202437 A <*> 0 0,3,30:1:1,0 1 1
#> 5 25202438 G <*> 0 0,3,34:1:1,0 1 1
#> 6 25202439 G <*> 0 0,3,33:1:1,0 1 1
#> 7 25202440 G <*> 0 0,3,34:1:1,0 1 1
#> 8 25202441 G <*> 0 0,3,33:1:1,0 1 1
#> 9 25202442 A <*> 0 0,3,32:1:1,0 1 1
#> 10 25202443 T <*> 0 0,3,31:1:1,0 1 1
#> # <e2><80><a6> with 8,907 more rows
## End(Not run)
jhrcook/KrasAlleleCna documentation built on May 28, 2019, 1:22 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Examples
Description
Parse the read-depth information of a VCF file produced by mpileup
Usage
1 | parse_vcf(fname)
|
Arguments
fname |
path to the file |
Value
a tibble
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | ## Not run:
# head of the VCF file
#> ##fileformat=VCFv4.2
#> ##FILTER=<ID=PASS,Description="All filters passed">
#> ##bcftoolsVersion=1.9+htslib-1.9
#> ##bcftoolsCommand=mpileup -Ov --annotate INFO/AD,FORMAT/AD,FORMAT/DP ...
#> ##reference=file:///n/no_backup2/dbmi/park/jc604/databases/reference_...
#> ##contig=<ID=chr1,length=248956422>
#> ##contig=<ID=chr2,length=242193529>
#> ##contig=<ID=chr3,length=198295559>
#> ##contig=<ID=chr4,length=190214555>
#> ##contig=<ID=chr5,length=181538259>
#> ##contig=<ID=chr6,length=170805979>
#> ##contig=<ID=chr7,length=159345973>
#> ##contig=<ID=chr8,length=145138636>
#> ##contig=<ID=chr9,length=138394717>
#> ##contig=<ID=chr10,length=133797422>
#> ##contig=<ID=chr11,length=135086622>
#> ##contig=<ID=chr12,length=133275309>
#> ##contig=<ID=chr13,length=114364328>
#> ##contig=<ID=chr14,length=107043718>
#> ##contig=<ID=chr15,length=101991189>
#> ##contig=<ID=chr16,length=90338345>
#> ##contig=<ID=chr17,length=83257441>
#> ##contig=<ID=chr18,length=80373285>
#> ##contig=<ID=chr19,length=58617616>
#> ##contig=<ID=chr20,length=64444167>
#> ##contig=<ID=chr21,length=46709983>
#> ##contig=<ID=chr22,length=50818468>
#> ##contig=<ID=chrX,length=156040895>
#> ##contig=<ID=chrY,length=57227415>
#> ##contig=<ID=chrM,length=16569>
#> ##contig=<ID=chr1_KI270706v1_random,length=175055>
#> ##contig=<ID=chr1_KI270707v1_random,length=32032>
#> ##contig=<ID=chr1_KI270708v1_random,length=127682>
#> ...
#> ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
#> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
#> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
#> ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic depths">
#> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TCGA-FZ-5924-01A-13D-1609-08
#> chr12 25202434 . A <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,29,841,0,0,60,3600,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,29:1:1,0
#> chr12 25202435 . G <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,31,961,0,0,60,3600,0,0,1,1,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,31:1:1,0
#> chr12 25202436 . C <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,28,784,0,0,60,3600,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,28:1:1,0
#> chr12 25202437 . A <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,30,900,0,0,60,3600,0,0,3,9,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,30:1:1,0
#> chr12 25202438 . G <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,4,16,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,34:1:1,0
#> chr12 25202439 . G <*> 0 . DP=1;AD=1,0;I16=1,0,0,0,33,1089,0,0,60,3600,0,0,5,25,0,0;QS=1,0;MQ0F=0 PL:DP:AD 0,3,33:1:1,0
#> ...
parse_vcf("example.vcf")
#> # A tibble: 8,917 x 7
#> start ref alt qual read_info num_high_qual_bas<e2><80><a6> allelic_depths
#> <dbl> <chr> <chr> <dbl> <chr> <chr> <chr>
#> 1 25202434 A <*> 0 0,3,29:1:1,0 1 1
#> 2 25202435 G <*> 0 0,3,31:1:1,0 1 1
#> 3 25202436 C <*> 0 0,3,28:1:1,0 1 1
#> 4 25202437 A <*> 0 0,3,30:1:1,0 1 1
#> 5 25202438 G <*> 0 0,3,34:1:1,0 1 1
#> 6 25202439 G <*> 0 0,3,33:1:1,0 1 1
#> 7 25202440 G <*> 0 0,3,34:1:1,0 1 1
#> 8 25202441 G <*> 0 0,3,33:1:1,0 1 1
#> 9 25202442 A <*> 0 0,3,32:1:1,0 1 1
#> 10 25202443 T <*> 0 0,3,31:1:1,0 1 1
#> # <e2><80><a6> with 8,907 more rows
## End(Not run)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.