adding new SCE classification --> Need to re-install MosaiCatcher C++ code!

Snake.config.json

@@ -2,11 +2,10 @@
     "chromosomes"   : ["chrX","chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22"],
 
     "reference"     : "/g/korbel/shared/datasets/refgenomes/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
-    "mosaicatcher"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/build/mosaicatcher",
+    "mosaicatcher"  : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/build/mosaicatcher",
     "plot_script"   : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/qc.R",
     "plot_segments" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/plot_segments.R",
     "sv_plot_script": "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/R/svs.R",
-    "sce_script"    : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/sce_utils/SCE.R",
     "samtools"      : "samtools",
     "bcftools"      : "bcftools",
 

Snakefile

@@ -361,10 +361,10 @@ rule determine_initial_strand_states:
     log:
         "log/{sample}/determine_initial_strand_states.txt"
     params:
-        sce_command = "Rscript " + config["sce_script"]
+        mc_command = config["mosaicatcher"]
     shell:
         """
-        {params.sce_command} {input} {output}
+        {params.mc_command} states -u -v -o {output} {input} 2>&1 > {log}
         """
 
 # Strandphaser needs a different input format which contains the path names to