Man page - vcfleftalign(1)
Packages contains this manual
- vcflib-api(1)
- vcfannotategenotypes(1)
- vcfcat(1)
- vcfgeno2alleles(1)
- vcfroc(1)
- vcfhethomratio(1)
- vcfcountalleles(1)
- vcfaddinfo(1)
- vcfrandomsample(1)
- vcfbreakmulti(1)
- vcfcheck(1)
- vcfsitesummarize(1)
- vcfdistance(1)
- vcfglbound(1)
- pyvcflib(1)
- vcfinfosummarize(1)
- vcflib(1)
- vcfnumalt(1)
- vcfsample2info(1)
- vcfkeepgeno(1)
- vcfgeno2haplo(1)
- vcfallelicprimitives(1)
- vcfindex(1)
- vcfecho(1)
- vcfwave(1)
- vcf2tsv(1)
- vcffixup(1)
- vcfremap(1)
- vcfnullgenofields(1)
- vcfoverlay(1)
- vcfremoveaberrantgenotypes(1)
- vcfflatten(1)
- vcfintersect(1)
- vcfprimers(1)
- vcfgenosamplenames(1)
- vcfafpath(1)
- vcfinfo2qual(1)
- vcfparsealts(1)
- vcffilter(1)
- vcfuniqalleles(1)
- vcfgenotypes(1)
- vcfsamplenames(1)
- vcfaltcount(1)
- vcfcombine(1)
- vcfuniq(1)
- vcf2dag(1)
- vcfgenotypecompare(1)
- vcfhetcount(1)
- vcfclassify(1)
- vcfkeepsamples(1)
- vcf2fasta(1)
- vcflength(1)
- vcfleftalign(1)
- vcfcommonsamples(1)
- vcfglxgt(1)
- vcfentropy(1)
- vcfrandom(1)
- vcfcreatemulti(1)
- vcfnulldotslashdot(1)
- vcfgenosummarize(1)
- vcfstats(1)
- vcfannotate(1)
- smoother(1)
- vcfstreamsort(1)
- vcfevenregions(1)
- vcfld(1)
- vcfkeepinfo(1)
- vcfqual2info(1)
- vcfremovesamples(1)
- abba-baba(1)
- vcfcleancomplex(1)
- vcfsamplediff(1)
Package: libvcflib-tools
apt-get install libvcflib-tools
apt-get install libvcflib-tools
Manuals in package:
Documentations in package:
Manual
VCFLEFTALIGN
NAMESYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS
NAME
vcfleftalign
SYNOPSIS
vcfleftalign options [file]
DESCRIPTION
Left-align indels and complex variants in the input using a pairwise ref/alt alignment followed by a heuristic, iterative left realignment process that shifts indel representations to their absolute leftmost (5’) extent.
OPTIONS
This is the same procedure used in the internal left alignment in
freebayes, and can be used when preparing VCF files for input to
freebayes to decrease positional representation differences between
the input alleles and left-realigned alignments.
options:
-r, --reference FILE Use this reference as a basis for realignment.
-w, --window N Use a window of this many bp when left aligning (150).
Left-aligns variants in the specified input file or stdin. Window
size is determined dynamically according to the entropy of the regions
flanking the indel. These must have entropy > 1 bit/bp, or be shorter
than ~5kb.
Type: transformation
EXIT VALUES
|
0 |
Success |
|||
|
not 0 |
Failure |
SEE ALSO
vcflib (1)
OTHER
LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.
AUTHORS
Erik Garrison and vcflib contributors.