n, -normalize-alleles Make REF and ALT alleles more compact if possible (e.g. H, -hard-filter Remove lines with FILTER anything else than PASS or "." f, -filter Apply filters, list is in the format flt1=value/flt2/flt3=value/etc. fill-type Annotate INFO/TYPE with snp,del,ins,mnp,complex fill-ICF (Re)Calculate Inbreeding Coefficient F, HWE, AC and AN fill-HWE (Re)Calculate HWE, AC and AN tags The descriptions can be read from a file, one annotation per line. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. When REF and ALT columns are present, only Present, it is assumed that TO equals to FROM. In this example indicates that the third column should be ignored. c, -columns The list of columns in the annotation file, e.g. a, -annotations The tabix indexed file with the annotations: CHR\tFROM+. Usage: cat in.vcf | vcf-annotate > out.vcf Requires tabix indexed file with annotations.Ĭurrently it can annotate ID, QUAL, FILTER and INFO columns, but will be extended on popular demand.įor examples of user-defined filters see online documentation or examples/filters.txt in vcftools distribution. (Read more) About: Annotates VCF file, adding filters or custom annotations. Some of the predefined filters take advantage of tags added by bcftools, the descriptions of the most frequently asked There are a number of predefined filters andĬustom filters can be easily added, see vcf-annotate -h for examples. The script is also routinely used to apply filters. d key=INFO,ID=ANN,Number=1,Type=Integer,Description='My custom annotation' \ To add custom annotations to VCF files, create TAB delimited file with annotationsĬompress the file (using bgzip annotations), index (using tabix -s 1 -b 2 -e 3 annotations.gz) andĬat in.vcf | vcf-annotate -a annotations.gz \ The script adds or removes filters and custom annotations to VCF files. This script has been discontinued, please use vcf-annotate instead. r, -refseq The reference sequence in fasta format indexed by samtools faidxįill-ref-md5 -i AS:NCBIM37,SP:"Mus\ Musculus" -r NCBIM37_um.fa -d NCBIM37_um.fa.dict in.vcf.gz įill missing rsIDs. i, -info Optional info on reference assembly (AS), species (SP), taxonomy (TX) Opened in append mode, existing records are not touched. d, -dictionary Where to read/write computed MD5s. Of the lightning fast tabix reheader functionality. The VCF file must be compressed and tabix indexed, as it takes advantage 'reference' and 'contig' tags into header as recommended by VCFv4.1. (Read more) About: The script computes MD5 sum of the reference sequence and inserts # Mask variants from the VCF file with N's and use lowercase for the bed file regionsįill-fs file.vcf -v mask.vcf -m lc -b mask.bedįill missing reference info and sequence MD5s into VCF header.įill-ref-md5 -i "SP:Homo\ Sapiens" -r ref.fasta in.vcf.gz -d ref.dict v, -vcf-mask Mask known variants in the flanking sequence, multiple files can be given (tabix indexed) With multiple files worksĪs a switch on the command line, see the example below m, -mask-char The character to use or "lc" for lowercase. c, -cluster Do self-masking of clustered variants within this range. b, -bed-mask Regions to mask (tabix indexed), multiple files can be given (Read more) About: Annotate VCF with flanking sequence (INFO/FS tag) The VCF files can be compressed and indexed using the following commandsįill or recalculate AN and AC INFO fields. Many of the Perl scripts require that the VCF files are compressed by bgzipĪnd indexed by tabix (both tools are part of the htslib/tabix package, Run any of the Perl scripts with the -help switch to obtain more help. The VCFtools in general have been used mainly with diploid data, but the Perl toolsĪim to support polyploid data as well. Nevertheless, the users are encouraged to use the latest versions VCFv4.1 or VCFv4.2. Support all versions of the VCF specification (3.2, 3.3, 4.0, 4.1 and 4.2), Of Perl scripts that can be used to perform common tasks with VCF files such asįile validation, file merging, intersecting, complements, etc. VCFtools contains a Perl API ( Vcf.pm) and a number A set of tools written in Perl and C++ for working with VCF files.
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