Important flag *sn_sites_to_genotype* in the configfile. This overwrites the...

Important flag *sn_sites_to_genotype* in the configfile. This overwrites the entry from *Snake.config.json*. The file it points to has to be provided by the user (too big to include into image)

Snake.config-singularity.json

 {
     "chromosomes"   : ["chrX","chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX"],
 
+    "snv_sites_to_genotype" : "snv_sites_to_genotype/ALL.chr1-22plusX_GRCh38_sites.20170504.renamedCHR.vcf.gz",
 
     "reference"     : "/reference.fa",
     "mosaicatcher"  : "mosaic",
@@ -10,12 +11,6 @@
     "samtools"      : "samtools",
     "bcftools"      : "bcftools",
 
-    "snv_calls"     : {
-        "C7_data"   : "external_info/regenSNVs_GRCh38sites_C7_chr1-22plusX.filtered.vcf.gz",
-        "RPE-BM510" : "external_info/regenSNVs_GRCh38sites_BM510_chr1-22plusX.filtered.vcf.gz",
-        "RPE1-WT"   : "external_info/regenSNVs_GRCh38sites_RPEWTstrandS_chr1-22plusX.filtered.vcf.gz"
-    },
-
     "variable_bins" : {
         "50000"     : "utils/variable_bins.GRCh38.50kb.bed",
         "100000"    : "utils/variable_bins.GRCh38.100kb.bed"