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¶

LICENSE¶

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

AUTHORS¶

Erik Garrison and vcflib contributors.