table of contents
SNP-SITES(1) | SNP-SITES(1) |
NAME¶
snp-sites - finds SNP sites from a multi FASTA alignment fileSYNOPSIS¶
snp-sites [-mvph] [-o output_filename] [input file]DESCRIPTION¶
This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in either of the following formats:•multi fasta alignment
•VCF
•relaxed phylip format
OPTIONS¶
-rOutput internal pseudo reference sequence
-m
Output a multi fasta alignment file (default)
-v
Output a VCF file
-p
Output a phylip file
-c
Only output columns containing exclusively ACGT
-b
Output monomorphic sites, useful for BEAST
-o
Specify an output filename
-h
Show help message
-V
Show version and exit
EXAMPLES¶
snp-sites my-alignment.aln
snp-sites my-gzipped-alignment.aln.gz
snp-sites -cb -o output_beast_format.aln inputfile.aln
FORMAT OF THE INPUT FILE¶
Input files should look like this:>reference_sequence aaccggtt >comparison_sequence AACCGGTT >another_comparison_sequence AACCGCTT
For more examples, visit: <https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data>