vcfremap

       Erik Garrison and vcflib contributors.

vcfremap (vcflib)                                                                                    VCFREMAP(1)

       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  align‐
       ment  parameters,  including context and entropy-dependent ones, influence variant classification and in‐
       terpretation.

0      Success

       not0  Failure

       Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.  MIT licensed.   Copyright  2020-2024  (C)
       Pjotr Prins.

vcfremap

              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

vcflib(1)

vcfremap options []