Sort final bed

EichlerLab · Feb 28, 2024 · f20e30b · f20e30b
1 parent 27e3512
commit f20e30b
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pipelines/summarize_flagger_output/workflow/Snakefile b/pipelines/summarize_flagger_output/workflow/Snakefile
@@ -123,7 +123,7 @@ rule liftover_bed:
         hrs=2,
     shell:
         """
-        cut -f 1,3,4,13 {input.paf} | sed 's/id:Z://' | sed 's/_TO.*//' | awk '{{if (NF == 4) print}}' > {output.bed}
+        cut -f 1,3,4,13 {input.paf} | sed 's/id:Z://' | sed 's/_TO.*//' | awk '{{if (NF == 4) print}}' | sort -k1,1 -k2,2n > {output.bed}
         """