VCFREMAP(1) vcfremap (VCF transformation) VCFREMAP(1) NAME vcfremap SYNOPSIS vcfremap options [] DESCRIPTION For each alternate allele, attempt to realign against the reference with lowered gap open penalty. If realignment is possible, adjust the cigar and reference/alternate alleles. Observe how different alignment parameters, including context and entropy-dependent ones, influence variant classifica- tion and interpretation. OPTIONS options: -w, --ref-window-size N align using this many bases flanking each side of the reference allele -s, --alt-window-size N align using this many flanking bases from the reference around each alternate allele -r, --reference FILE FASTA reference file, required with -i and -u -m, --match-score N match score for SW algorithm -x, --mismatch-score N mismatch score for SW algorithm -o, --gap-open-penalty N gap open penalty for SW algorithm -e, --gap-extend-penalty N gap extension penalty for SW algorithm -z, --entropy-gap-open use entropy scaling for the gap open penalty -R, --repeat-gap-extend N penalize non-repeat-unit gaps in repeat sequence -a, --adjust-vcf TAG supply a new cigar as TAG in the output VCF 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. vcfremap (vcflib) VCFREMAP(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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