1% VCF2FASTA(1) vcf2fasta (vcflib) | vcf2fasta (VCF transformation)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**vcf2fasta**
7
8# SYNOPSIS
9
10**vcf2fasta** [options] [file]
11
12# DESCRIPTION
13
14Generates 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.
15
16
17
18# OPTIONS
19
20```
21
22options:
23    -f, --reference REF     Use this reference when decomposing samples.
24    -p, --prefix PREFIX     Affix this output prefix to each file, none by default
25    -P, --default-ploidy N  Set a default ploidy for samples which do not have information in the first record (2).
26
27
28Type: transformation
29
30```
31
32
33
34
35
36# EXIT VALUES
37
38**0**
39: Success
40
41**not 0**
42: Failure
43
44# SEE ALSO
45
46
47
48[vcflib](./vcflib.md)(1)
49
50
51
52# OTHER
53
54## Source code
55
56[vcf2fasta.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcf2fasta.cpp)
57
58# LICENSE
59
60Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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