Forking can dramatically improve runtime. However running VEP on unsorted input files slows down the tool and requires more memory. Generate a plain text stats file in place of the HTML.įile name to write warnings and errors to.Įxtend the maximum Structural Variant size VEP can process. Of the VEP run - the file name must end ".htm" or ".html".ĭefault = "variant_effect_output.txt_summary.html"ĭon't generate a stats file. This is an HTML file containing a summary You can force the overwrite of the existingįile by using this flag. 'STDOUT' as the output file name - this will force quiet mode.īy default, VEP will fail with an error if the outputįile already exists. Results can write to STDOUT by specifying Using this option youĬan specify the input file is Ensembl, VCF, IDs, HGVS, SPDI or region format.Ĭan use compressed version (gzipped) of any file format listed above. "ensembl", "vcf", "hgvs", "id", "region", "spdi".īy default, VEP auto-detects the input file format. Or HGVS notation quickly to vep: -input_data rs699 May be used, for example, to input a single rsID If not specified, VEP will attempt to read from STDIN. Installed, this will be chosen by default. If not specified and you have only 1 assembly version The cache, you must have the appropriate assembly's cache file Select the assembly version to use if more than one available. Registry does not have to load all available database aliases on Latin name can speed up initial database connection as the Shortcut flag to switch on all of the following: Will output lines that can be copied to a config file that canīe loaded in on the next run using -config. Normal and running VEP in verbose ( -v) mode. YouĬan create a quick version file of this by setting the flags as Turn by any options specified on the command line. Those specified in a config file using -config, and in Any options in this file will be overridden by $HOME/.vep/vep.ini (or equivalent directory if using Should consist of whitespace-separated pairs of option names andĪ config file can also be implicitly read save the file as Load configuration options from a config file.
#Annotate a vcf file with atext file code#
The extra alt allele is given the number 2, so in this case if an individual had the genotype CT then their genotype code would be 0/2.įull detail is given in the official VCF specification page.Print out a bit more information while running. Occasionally you will have multi allelic positions, where you have more than one alternate allele, and therefore the field will look like: Ref Alt
0/0 is referred to as homozygous reference, and 1/1 as homozygous alternative.Ġ|1 and 1|0 do mean something different, since the pipe symbol | tell us the order of the alleles matters. However, in practice, a heterozygous genotype is always written as 0/1 as a matter of convention. The / symbol tells you the genotype is unphased. It's just a simplified way of expressing the different alleles.Ġ/1 and 1/0 functionally mean the same thing (that the individual is a heterozygote) - since the genotype is unphased, the alleles aren't ordered. for genotype in VCFĠ and 1 is just a way of coding the reference (0) and alternate (1) allele. What Does Genotype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent?ĭifference between 0/0 and. In general, the name homo means the same, and hetero means different, in the context of genotypes.ĭanecek P, Auton A, Abecasis G, et al. This is called homozygous alternate genotype. This means that the same ALT allele (either C, or G, or CA) is present in 2 copies. įinally, these are some examples of HOM_ALT: A C 1/1 Note that it is not enclosed in square brackets in the vcf file format: A C,CA 1/2. It is a heterozygous genotype composed of two different ALT alleles, or HET_ALT. This means there are no reference alleles here at all, only alternate alleles. When ALT=C,CA, the GT is probably 1/2, because there are 2 alternate alleles, and I assume we continue with the same chromosome present in 2 copies. The convention is write GT field in ascending order, so 0/1 rather than 1/0. This means that you have A on one copy of this locus, and G on another. When ALT=G, and the GT column is 0/1, this means that you have 1 reference allele (0), and 1 alternate allele (1). There are 2 copies of each allele in the human genome in non-sex chromosomes chr1-chr22, hence 0/0, or homozygous reference or HOM_REF. When the alternate allele is also A, the genotype GT is reference, or 0. In your case, the reference allele, here a single nucleotide, is A. Quoting from there, "GT, genotype, encodes alleles as numbers: 0 for the reference allele, 1 for the first allele listed in ALT column, 2 for the second allele listed in ALT and so on." You can get most of the info from this paper.
0 kommentar(er)
