vcf2txt {saasCNV} | R Documentation |
Covert VCF File to A Data Frame
Description
It parses a VCF file and extract necessary information for CNV analysis.
Usage
vcf2txt(vcf.file, normal.col = 10, tumor.col = 11, MQ.cutoff = 30)
Arguments
vcf.file |
vcf file name. |
normal.col |
the number of the column in which the genotype and read depth information of normal tissue are located in the vcf file. |
tumor.col |
the number of the column in which the genotype and read depth information of tumor tissue are located in the vcf file. |
MQ.cutoff |
the minimum criterion of mapping quality. |
Details
Note that the first 9 columns in vcf file are mandatory, followed by the information for called variant starting from the 10th column.
Value
A data frame of detailed information about each variant, including chrosome position, reference and alternative alleles, genotype and read depth carrying reference and alternative alleles for normal and tumor respectively.
Author(s)
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
References
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., et al. (2011) The variant call format and VCFtools. Bioinformatics, 27:2156–2158.
http://www.1000genomes.org/node/101
Examples
## Not run:
## an example VCF file from WES
## download WES_example.vcf.gz
url <- "https://zhangz05.u.hpc.mssm.edu/saasCNV/data/WES_example.vcf.gz"
tryCatch({download.file(url=url, destfile="WES_example.vcf.gz")
}, error = function(e) {
download.file(url=url, destfile="WES_example.vcf.gz", method="curl")
})
## If download.file fails to download the data, please manually download it from the url.
## convert VCf file to a data frame
vcf_table <- vcf2txt(vcf.file="WES_example.vcf.gz", normal.col=9+1, tumor.col=9+2)
## see how vcf_table looks like
## download vcf_table.txt.gz
url <- "https://zhangz05.u.hpc.mssm.edu/saasCNV/data/vcf_table.txt.gz"
tryCatch({download.file(url=url, destfile="vcf_table.txt.gz")
}, error = function(e) {
download.file(url=url, destfile="vcf_table.txt.gz", method="curl")
})
## If download.file fails to download the data, please manually download it from the url.
vcf_table <- read.delim(file="vcf_table.txt.gz", as.is=TRUE)
head(vcf_table)
## End(Not run)