VCFINTERSECT(1) vcfintersect (VCF transformation) VCFINTERSECT(1) NAME vcfintersect SYNOPSIS vcfintersect options [] DESCRIPTION VCF 1.0.12 set analysis OPTIONS options: -b, --bed FILE use intervals provided by this BED file -R, --region REGION use 1-based tabix-style region (e.g. chrZ:10-20), multiples allowed -S, --start-only don't use the reference length information in the record to determine overlap status, just use the start posiion -v, --invert invert the selection, printing only records which would not have been printed out -i, --intersect-vcf FILE use this VCF for set intersection generation -u, --union-vcf FILE use this VCF for set union generation -w, --window-size N compare records up to this many bp away (default 30) -r, --reference FILE FASTA reference file, required with -i and -u -l, --loci output whole loci when one alternate allele matches -m, --ref-match intersect on the basis of record REF string -t, --tag TAG attach TAG to each record's info field if it would intersect -V, --tag-value VAL use this value to indicate that the allele is passing '.' will be used otherwise. default: 'PASS' -M, --merge-from FROM-TAG -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG in the current file. For bed-vcf intersection, alleles which fall into the targets are retained. Haplotype aware intersection, union and complement. Use for intersection and union of VCF files: unify on equivalent alleles within window-size bp as determined by haplotype comparison alleles. type: transformation EXIT VALUES 0 Success not 0 Failure SEE ALSO vcflib(1) OTHER LICENSE Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. MIT li- censed. Copyright 2020-2025 (C) Pjotr Prins. AUTHORS Erik Garrison and vcflib contributors. vcfintersect (vcflib) VCFINTERSECT(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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