From 3ca02902a254a61b3f4e2709d1ae3b7f05d78e31 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Fri, 15 Jun 2018 22:40:51 +0200
Subject: [PATCH] Use more recent SV plot script + do not black list counts
based initially
---
Snake.config.json | 2 +-
Snakefile | 9 +++++++--
2 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 74ac5cf..ae87ff7 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -5,7 +5,7 @@
"mosaicatcher" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/build/mosaicatcher",
"plot_script" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/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",
+ "sv_plot_script": "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/chrom.R",
"norm_script" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/norm.R",
"samtools" : "samtools",
"bcftools" : "bcftools",
diff --git a/Snakefile b/Snakefile
index b79e7e1..de8fde6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -179,9 +179,11 @@ rule plot_SV_calls:
segments = "segmentation2/{sample}/{windows}.{bpdens}.txt"
output:
"sv_calls/{sample}/{windows}.{bpdens}/{method}.{chrom}.pdf"
+ params:
+ sv_plot_script = config["sv_plot_script"]
shell:
"""
- Rscript utils/chrom.R segments={input.segments} strand={input.strand} calls={input.calls} {input.counts} {wildcards.chrom} {output}
+ Rscript {params.sv_plot_script} segments={input.segments} strand={input.strand} calls={input.calls} {input.counts} {wildcards.chrom} {output}
"""
rule plot_SV_calls_simulated:
@@ -193,9 +195,11 @@ rule plot_SV_calls_simulated:
truth = "simulation/variants/genome{seed}-{window}.txt"
output:
"sv_calls/simulation{seed}-{window}/{window}_fixed.{bpdens}/{method}.{chrom}.pdf"
+ params:
+ sv_plot_script = config["sv_plot_script"]
shell:
"""
- Rscript utils/chrom.R segments={input.segments} strand={input.strand} truth={input.truth} calls={input.calls} {input.counts} {wildcards.chrom} {output}
+ Rscript {params.sv_plot_script} segments={input.segments} strand={input.strand} truth={input.truth} calls={input.calls} {input.counts} {wildcards.chrom} {output}
"""
@@ -248,6 +252,7 @@ rule mosaic_count_fixed:
"""
{params.mc_command} count \
--verbose \
+ --do-not-blacklist-hmm \
-o {output.counts} \
-i {output.info} \
-x {input.excl} \
--
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