vcfremap1

Usage

Overview

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 classification 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 status

0

Success

not 0

Failure

Other