README.md

Usage:  
-clone repo into empty directory  
-mkdir data  
-mkdir data/samples_raw  
-mkdir data/samples_raw/{sample_name}  
-for each sample, place the fastqs for  
 that sample in data/samples_raw/{sample_name}/  
-specify path to reference genome in workflow/config/config.yaml  

-run with 'snakemake --use-conda'  

Output file structure:    
└────data/  
     ├────mapped_reads/  
     |    ├────{sample_name}.bam  
     |    └────{sample_name}.bam.bai  
     |  
     ├────samples/  
     |    └────{sample_name}.fastq.gz  
     |  
     ├────samples_raw/  
     |    └────{sample_name}/  
     |  
     └────variants/  
          └────{sample_name}_variants.vcf