From e35d1aadadbbd185d474376fe50df737a5721dcc Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Sun, 7 Oct 2018 09:47:20 +0200
Subject: [PATCH] Decrease cutoff for adding an extra SCE from 20Mb to 5Mb.
Should help avoiding wrong inversion calls towards the end of a chromosome.
---
Snakefile | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 291d83c..80b43c5 100644
--- a/Snakefile
+++ b/Snakefile
@@ -554,8 +554,9 @@ rule segmentation_selection:
params:
cellnames = lambda wc: ",".join(cell for cell in CELL_PER_SAMPLE[wc.sample]),
sce_min_distance = 500000,
+ additional_sce_cutoff = 5000000,
shell:
- "./utils/detect_strand_states.py --sce_min_distance {params.sce_min_distance} --min_diff_jointseg {wildcards.min_diff_jointseg} --min_diff_singleseg {wildcards.min_diff_singleseg} --output_jointseg {output.jointseg} --output_singleseg {output.singleseg} --output_strand_states {output.strand_states} --samplename {wildcards.sample} --cellnames {params.cellnames} {input.info} {input.counts} {input.jointseg} {input.singleseg} > {log} 2>&1"
+ "./utils/detect_strand_states.py --sce_min_distance {params.sce_min_distance} --sce_add_cutoff {params.additional_sce_cutoff} --min_diff_jointseg {wildcards.min_diff_jointseg} --min_diff_singleseg {wildcards.min_diff_singleseg} --output_jointseg {output.jointseg} --output_singleseg {output.singleseg} --output_strand_states {output.strand_states} --samplename {wildcards.sample} --cellnames {params.cellnames} {input.info} {input.counts} {input.jointseg} {input.singleseg} > {log} 2>&1"
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