This is especially relevant when using the RefSeq cache, see documentation for more details. Use this flag to force VEP to replace the provided reference allele with sequence derived from the overlapped transcript. Enables -use_transcript_ref add -use_given_ref to override this behaviour.īy default VEP uses the reference allele provided in the input file to calculate consequences for the provided alternate allele(s). Used to correct RefSeq transcript models. NotĪDVANCED Use BAM file of sequence alignments to correct transcript models not derived from reference genome sequence. Requires a FASTA file of genomic sequence. Use GTF transcript annotations in as an annotation source. Use GFF transcript annotations in as an annotation source. Supplying the -custom flag multiple times. Not used byĪdd custom annotation to the output. Multiple plugins can be used by supplying the Plugins subdirectory of the VEP cache directory (defaults to Plugin modules should be installed in the Higher to use more memory with a faster run time. Lower to use less memory at the expense of longer run time, and Variants that are read in to memory simultaneously. Sets the internal buffer size, corresponding to the number of Show source version information for selected cache and quit VEP/Ensembl version may be 88 and the Ensembl Genomes version 35. Version numbers do not match Ensembl versions. This should be used with Ensembl Genomes caches since their Use a different cache version than the assumed default (the VEP Add -refseq or -merged to use the refseq or merged cache, (if installed).
Not used by defaultĮnables use of the cache. 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. Print out a bit more information while running.
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