From 4987cd6ee4330562dcfe0a5116452abb8fac7843 Mon Sep 17 00:00:00 2001
From: maryamghr <maryam@lap-13-67.mmci.uni-saarland.de>
Date: Wed, 21 Feb 2018 17:47:02 +0100
Subject: [PATCH] added a rule for heatmap plotting
---
Snakefile | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/Snakefile b/Snakefile
index 4430c12..99484d7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -375,6 +375,20 @@ rule run_sv_classification:
maximumCN=4 \
utils/R-packages2/ > {log} 2>&1
"""
+
+rule convert_SVprob_output:
+ input:
+ haplotypeProbs = "sv_probabilities/{sample}/{windows}.{bpdens}/allSegCellProbs.table",
+ genotypeProbs = "sv_probabilities/{sample}/{windows}.{bpdens}/allSegCellGTprobs.table",
+ info = "counts/{sample}/{windows}.info",
+ bamNames = "sv_probabilities/{sample}/{windows}.{bpdens}/bamNames.txt"
+ output:
+ "sv_probabilities/{sample}/{windows}.{bpdens}/final_plots/"
+ log:
+ "log/{sample}/final.plots.{windows}.{bpdens}.txt"
+ script:
+ "utils/plot_heatmap.R"
+
rule convert_SVprob_output:
input:
probs = "sv_probabilities/{sample}/{windows}.{bpdens}/allSegCellProbs.table",
--
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