vcf2fasta1

Usage

Overview

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 status

0

Success

not 0

Failure

Other