Liftoff bed no paf

EichlerLab · May 30, 2024 · a4ddbd2 · a4ddbd2
1 parent 1eb9195
commit a4ddbd2
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/pipelines/summarize_flagger_output/workflow/Snakefile b/pipelines/summarize_flagger_output/workflow/Snakefile
@@ -115,7 +115,6 @@ rule liftover_coords:
     shell:
         """
         liftOver <(cut -f 1-4 {input.flagger_bed} | tail -n +2 ) {input.chain_file} {output.new_bed} {output.unmapped_bed} 
-        rustybam liftover -b  -q {input.paf} > {output.paf}
         awk '{{s+=$3-$2;}} END {{print "Total Flagger bases before liftover: " s}}' {input.flagger_bed}
         awk '{{s+=$9-$8;}} END {{print "Total bases after liftover: " s}}' {output.new_bed}
         awk '{{s+=$9-$8;}} END {{print "Unmapped bases after liftover: " s}}' {output.unmapped_bed}
@@ -124,7 +123,7 @@ rule liftover_coords:
 
 rule liftover_bed:
     input:
-        paf=rules.liftover_coords.output.paf,
+        paf=rules.liftover_coords.output.new_bed,
     output:
         bed="results/converted_bed/{sample}.bed",
     threads: 1