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% VCF2FASTA(1) vcf2fasta (vcflib) | vcf2fasta (VCF transformation) % Erik Garrison and vcflib contributors

NAME

vcf2fasta

SYNOPSIS

vcf2fasta [options] [file]

DESCRIPTION

Generates sample_seq:N.fa for each sample, reference sequence, and chromosomal copy N in [0,1... ploidy]. Each sequence in the fasta file is named using the same pattern used for the file name, allowing them to be combined.

OPTIONS



options:
    -f, --reference REF     Use this reference when decomposing samples.
    -p, --prefix PREFIX     Affix this output prefix to each file, none by default
    -P, --default-ploidy N  Set a default ploidy for samples which do not have
                            information in the first record (2).
    -n VAL                  Set string value to output for missing calls

Type: transformation

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

vcf2fasta.cpp

LICENSE

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