Sometimes you have variant calls as vcf files. Bushwalk takes the vcf files and prepares the data of each sample for input into the snippy-core module of Snippy with the intended use to creat a multisequence alignment. We're going on a bushwalk!
- samtools
- bcftools
- Lodestone outputs vcf files in their own directory under the file structure ID/lodestone/
- Reference file paired with the vcf file: Needs to be in FASTA format and be only the chromosome
- A file containing all the IDs of the samples corresponding. Each sample ID will be on a new line.
usage: bushwalk.py [options] reference ids
Run Bushwalk. A program to parse the output of Lodestone for input into
snippy-core
positional arguments:
N Provide the reference for snippy [Required]
N IDs of paired reads files [Required]
optional arguments:
-h, --help show this help message and exit
-d [N], --dirpath [N]
Input directory of Lodestone results. End with a
forward slash. Eg. /temp/fasta/ [Required]
-o [N], --outdir [N] Output directory. End with a forward slash. Eg.
/temp/fasta/; Default to use current directory.
Bushwalk will generate:
- A new VCF file containing only SNV calls
- A SNV consensus fasta file