ExtractSNPs

Extract SNPs from genes of interest for Candida auris.

Prerequisite

Perl 5

Files

Genome annotation in GFF format
Variants.vcf
Genelist.txt

Genelist.txt is formatted as follows
(tab separated gene symbols and gene IDs used in Genome annotation file)

FUR1 B9J08_004076
TAC1B B9J08_004820
ERG2 B9J08_004943
ERG3 B9J08_003737
ERG5 B9J08_002349

How to use

To run the script, you might need to:

1. In Command Prompt (Windows) or Terminal (MacOS)
   
2. Type and run the command perl /PATH/to/SNP.filter.pl /PATH/to/Genome.gff /PATH/to/Genelist.txt /PATH/to/Variants.vcf
   

Output

output.txt containing variants in genes of interest will be generated in the current directory.