VCF2FASTA(1) vcf2fasta (VCF transformation) VCF2FASTA(1)

vcf2fasta

vcf2fasta options [file]

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:
    -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

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vcflib(1)

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.

Erik Garrison and vcflib contributors.

vcf2fasta (vcflib)