Convert SNP data in a somatypus VCF file to an alignment in Fasta format
This is a D program, and can be built using dub. The binary in the repo was built on Ubuntu 12.04.5 LTS using the command
dub build --compiler=ldc2 --build=release
Usage: vcfToFasta [--help] [--excludeInvariant] [--useGenotypeInfo]
[--ambiguityIsRef] [--fullContext] [--min_total_cov=<uint>]
[--min_alt_cov=<uint>] vcffile
Positional arguments:
vcffile VCF file (SNPs) to convert to alignment
Optional arguments:
--help, -h This help information
--excludeInvariant, -e
Filter out invariant sites from the alignment
--useGenotypeInfo, -g
Use the genotype information in the VCF file to confirm variant
sites, rather than numerical filters (default = off)
--ambiguityIsRef, -r
Ambiguous calls are conservatively called as the reference
base. If switched off, sites are called as the IUPAC ambiguity
code standing for Ref/Base (default = off)
--fullContext, -f
EXPERIMENTAL: output in a format that carries triplet sequence
context information. Each triplet is encoded as its position in
the alphabetical list [AAA, AAC, AAG, ... TTT] +63, converted
to ascii. Not compatible with ambiguity codes, so enforces
ambiguityIsRef to be switched on when fullContext is active
--min_total_cov, -c <uint>
Minimum number of reads (total) needed to consider as a
potentially variant site (default = 10)
--min_alt_cov, -a <uint>
Minimum number of variant-containing reads needed to confirm as
a variant site (default = 5)