VCFLEFTALIGN(1) vcfleftalign (VCF transformation) VCFLEFTALIGN(1) 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 2011-2025 (C) Erik Garrison and vcflib contributors. MIT li- censed. Copyright 2020-2025 (C) Pjotr Prins. AUTHORS Erik Garrison and vcflib contributors. vcfleftalign (vcflib) VCFLEFTALIGN(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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