Man page - vcfcleancomplex(1)

Packages contains this manual

Package: libvcflib-tools
apt-get install libvcflib-tools

Manuals in package:

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)

Documentations in package:

libvcflib-tools

Manual

VCFCLEANCOMPLEX

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

NAME

vcfcleancomplex

SYNOPSIS

vcfcleancomplex

DESCRIPTION

Removes reference-matching sequence from complex alleles and adjusts records to reflect positional change.

OPTIONS

Generate a VCF stream in which 'long' non-complexalleles have their position corrected.
assumes that VCF records can't overlap 5'->3'

Type: transformation

EXIT VALUES

	0		Success
	not 0		Failure

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.