snpgdsVCF2GDS_R: Reformat a VCF file (R implementation)
In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
Reformat a Variant Call Format (VCF) file
Usage
1
2
3
4
snpgdsVCF2GDS_R(vcf.fn, out.fn, nblock=1024,
method = c("biallelic.only", "copy.num.of.ref"),
compress.annotation="LZMA_RA", snpfirstdim=FALSE, option = NULL,
verbose=TRUE)
Arguments
vcf.fn
the file name of VCF format, vcf.fn can be a vector,
see details
out.fn
the output gds file
nblock
the buffer lines
method
either "biallelic.only" by default or "copy.num.of.ref",
see details
compress.annotation
the compression method for the GDS variables,
except "genotype"; optional values are defined in the function
add.gdsn
snpfirstdim
if TRUE, genotypes are stored in the individual-major
mode, (i.e, list all SNPs for the first individual, and then list all
SNPs for the second individual, etc)
option
NULL or an object from snpgdsOption,
see details
verbose
if TRUE, show information
Details
GDS – Genomic Data Structures used for storing genetic array-oriented
data, and the file format used in the gdsfmt package.
VCF – The Variant Call Format (VCF), which is a generic format for storing
DNA polymorphism data such as SNPs, insertions, deletions and
structural variants, together with rich annotations.
If there are more than one file name in vcf.fn, snpgdsVCF2GDS
will merge all dataset together once they all contain the same samples. It is
useful to combine genetic data if VCF data are divided by chromosomes.
method = "biallelic.only": to exact bi-allelic and polymorhpic
SNP data (excluding monomorphic variants);
method = "biallelic.only": to exact bi-allelic and polymorhpic SNP
data; method = "copy.num.of.ref": to extract and store dosage (0, 1, 2)
of the reference allele for all variant sites, including bi-allelic SNPs,
multi-allelic SNPs, indels and structural variants.
Haploid and triploid calls are allowed in the transfer, the variable
snp.id stores the original the row index of variants, and the variable
snp.rs.id stores the rs id.
The user could use option to specify the range of code for autosomes.
For humans there are 22 autosomes (from 1 to 22), but dogs have 38 autosomes.
Note that the default settings are used for humans. The user could call
option = snpgdsOption(autosome.end=38) for importing the VCF file of dog.
It also allows defining new chromosome coding, e.g.,
option = snpgdsOption(Z=27), then "Z" will be replaced by the number 27.
Value
None.
Author(s)
Xiuwen Zheng
References
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA,
Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R;
1000 Genomes Project Analysis Group.
Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7.
See Also
snpgdsVCF2GDS_R, snpgdsOption,
snpgdsBED2GDS
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
# The VCF file
vcf.fn <- system.file("extdata", "sequence.vcf", package="SNPRelate")
cat(readLines(vcf.fn), sep="\n")
snpgdsVCF2GDS_R(vcf.fn, "test1.gds", method="biallelic.only")
snpgdsSummary("test1.gds")
snpgdsVCF2GDS_R(vcf.fn, "test2.gds", method="biallelic.only")
snpgdsSummary("test2.gds")
snpgdsVCF2GDS_R(vcf.fn, "test3.gds", method="copy.num.of.ref")
snpgdsSummary("test3.gds")
snpgdsVCF2GDS_R(vcf.fn, "test4.gds", method="copy.num.of.ref")
snpgdsSummary("test4.gds")
Example output
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
[1] 1
Mon Feb 11 21:49:39 2019 Done.
The file name: /work/tmp/test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
[1] 1
Mon Feb 11 21:49:39 2019 Done.
The file name: /work/tmp/test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
Mon Feb 11 21:49:39 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: /work/tmp/test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
Mon Feb 11 21:49:39 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: /work/tmp/test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
Reformat a Variant Call Format (VCF) file
Usage
1 2 3 4 | snpgdsVCF2GDS_R(vcf.fn, out.fn, nblock=1024,
method = c("biallelic.only", "copy.num.of.ref"),
compress.annotation="LZMA_RA", snpfirstdim=FALSE, option = NULL,
verbose=TRUE)
|
Arguments
vcf.fn |
the file name of VCF format, |
out.fn |
the output gds file |
nblock |
the buffer lines |
method |
either "biallelic.only" by default or "copy.num.of.ref", see details |
compress.annotation |
the compression method for the GDS variables,
except "genotype"; optional values are defined in the function
|
snpfirstdim |
if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc) |
option |
|
verbose |
if TRUE, show information |
Details
GDS – Genomic Data Structures used for storing genetic array-oriented data, and the file format used in the gdsfmt package.
VCF – The Variant Call Format (VCF), which is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations.
If there are more than one file name in vcf.fn, snpgdsVCF2GDS
will merge all dataset together once they all contain the same samples. It is
useful to combine genetic data if VCF data are divided by chromosomes.
method = "biallelic.only": to exact bi-allelic and polymorhpic
SNP data (excluding monomorphic variants);
method = "biallelic.only": to exact bi-allelic and polymorhpic SNP
data; method = "copy.num.of.ref": to extract and store dosage (0, 1, 2)
of the reference allele for all variant sites, including bi-allelic SNPs,
multi-allelic SNPs, indels and structural variants.
Haploid and triploid calls are allowed in the transfer, the variable
snp.id stores the original the row index of variants, and the variable
snp.rs.id stores the rs id.
The user could use option to specify the range of code for autosomes.
For humans there are 22 autosomes (from 1 to 22), but dogs have 38 autosomes.
Note that the default settings are used for humans. The user could call
option = snpgdsOption(autosome.end=38) for importing the VCF file of dog.
It also allows defining new chromosome coding, e.g.,
option = snpgdsOption(Z=27), then "Z" will be replaced by the number 27.
Value
None.
Author(s)
Xiuwen Zheng
References
The variant call format and VCFtools. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7.
See Also
snpgdsVCF2GDS_R, snpgdsOption,
snpgdsBED2GDS
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # The VCF file
vcf.fn <- system.file("extdata", "sequence.vcf", package="SNPRelate")
cat(readLines(vcf.fn), sep="\n")
snpgdsVCF2GDS_R(vcf.fn, "test1.gds", method="biallelic.only")
snpgdsSummary("test1.gds")
snpgdsVCF2GDS_R(vcf.fn, "test2.gds", method="biallelic.only")
snpgdsSummary("test2.gds")
snpgdsVCF2GDS_R(vcf.fn, "test3.gds", method="copy.num.of.ref")
snpgdsSummary("test3.gds")
snpgdsVCF2GDS_R(vcf.fn, "test4.gds", method="copy.num.of.ref")
snpgdsSummary("test4.gds")
|
Example output
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
[1] 1
Mon Feb 11 21:49:39 2019 Done.
The file name: /work/tmp/test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
[1] 1
Mon Feb 11 21:49:39 2019 Done.
The file name: /work/tmp/test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
Mon Feb 11 21:49:39 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: /work/tmp/test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Mon Feb 11 21:49:39 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: /usr/local/lib/R/site-library/SNPRelate/extdata/sequence.vcf
Mon Feb 11 21:49:39 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: /work/tmp/test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
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