Decrease cutoff for adding an extra SCE from 20Mb to 5Mb. Should help avoiding...

Decrease cutoff for adding an extra SCE from 20Mb to 5Mb. Should help avoiding wrong inversion calls towards the end of a chromosome.

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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