update generate_synthetic_genomes

The PBS script for generating the synthetic genomes to simulate off of is updated in this commit to point to the correct sacCer3 VCF files that contain ALL variants, and not just the subset of variants unique to the strain. The change in reference VCF files for the sacCer3 default run in a prior update precipitated the need for this update.

Author: owlang

paper/SyntheticStrain/job/generate_synthetic_genomes.sh

@@ -1,9 +1,9 @@
 #!/bin/bash
 
-# This script makes genomes to simulate from. Two yeast and two human genomes each with variants from VCF incorporated into sequence
+# This script makes genomes to simulate from. Two yeast and two human genomes each with a different variant profile based on their respective full sized VCF files
 
 ADDSNPS=scripts/add_VCF_into_Genomic_FASTA.py
-SVCF=../db/sacCer3_VCF
+SVCF=../db/sacCer3_VCF/full_VCF
 HVCF=../db/hg19_VCF
 [ -d synthetic_genome ] || mkdir synthetic_genome