Removing extra octopus filter that results in lower recall

Author: skchronicles

workflow/rules/somatic.smk

@@ -214,9 +214,8 @@ rule octopus_filter:
     input:
         vcf  = join(workpath, "octopus", "somatic", "{name}.octopus.unfiltered.vcf"),
     output:
-        vcfa  = join(workpath, "octopus", "somatic", "{name}.octopus.PASS.vcf"),
-        vcfb  = join(workpath, "octopus", "somatic", "{name}.octopus.SOMATIC.vcf"),
-        vcfc  = join(workpath, "octopus", "somatic", "{name}.octopus.SOMATIC_PASS.vcf"),
+        vcfa    = join(workpath, "octopus", "somatic", "{name}.octopus.PASS.vcf"),
+        vcfb    = join(workpath, "octopus", "somatic", "{name}.octopus.SOMATIC.vcf"),
         vcfsort = join(workpath, "octopus", "somatic", "{name}.octopus.vcf"),
     params: 
         genome = config['references']['GENOME'],
@@ -241,18 +240,11 @@ rule octopus_filter:
         '( $1 ~ /^#/ ) || ( $8 ~ /SOMATIC/ ) {{print}}' \\
         {output.vcfa} \\
         > {output.vcfb}
-    
-    bcftools filter \\
-        -i 'FMT/FT[0:0]=="PASS"' \\
-        {output.vcfb} \\
-        | bcftools filter \\
-            -i '{params.bcftools_filter_i_option}' \\
-            -o {output.vcfc}
-    
+
     bcftools sort \\
         -o {output.vcfsort} \\
         -O v \\
-        {output.vcfc}
+        {output.vcfb}
     """
 
 
@@ -1130,6 +1122,7 @@ rule somatic_selectvar:
         {output.filt}
     """
 
+
 rule somatic_merge_tumor:
     """Data-processing step to post-process vcf file generated by all the
     somatic callers. This step takes filtered tumor sample callsets from