manta FILTER==PASS and any cnv with 90% overlap

analyses/copy_number_consensus_call/README.md

@@ -53,12 +53,14 @@ The per-sample pipeline revolves around the use of Snakemake to run analysis for
 4) Run the Snakemake pipeline to perform analysis **per sample**. 
 5) Filter for any CNVs that are over a certain **SIZE_CUTOFF** (default 3000 bp)
 6) Filter for any **significant** CNVs called by Freec (default pval = 0.01)
-7) Filter out any CNVs that overlap 50% or more with **Immunoglobulin, telomeric, centromeric, seg_dup regions** as found in the file `ref/cnv_excluded.bed`
-8) Merge any CNVs of the same sample and call method if they **overlap or within 10,000 bp** (We consider CNV calls within 10,000 bp the same CNV)
-9) Reformat the columns of the files (So the info are easier to read)
-10) **Call consensus** by comparing CNVs from 2 call methods at a time. 
-
-Since there are 3 callers, there were 3 comparisons: `manta-cnvkit`, `manta-freec`, and `cnvkit-freec`. If a CNV from 1 caller **overlaps 50% or more** with at least 1 CNV from another caller, the common region of the overlapping CNV would be the new CONSENSUS CNV.
+7) Filter to keep manta calls that PASS all filters
+8) Filter out any CNVs that overlap 50% or more with **Immunoglobulin, telomeric, centromeric, seg_dup regions** as found in the file `ref/cnv_excluded.bed`
+9) Merge any CNVs of the same sample and call method if they **overlap or within 10,000 bp** (We consider CNV calls within 10,000 bp the same CNV)
+10) Reformat the columns of the files (So the info are easier to read)
+11) **Call consensus** by comparing CNVs from 2 call methods at a time. 
+
+Since there are 3 callers, there were 3 comparisons: `manta-cnvkit`, `manta-freec`, and `cnvkit-freec`. If a CNV from 1 caller **50% or more reciprocal overlaps** with at least 1 CNV from another caller,
+  **OR any CNV in 1** caller overlaps 90% or more in another to gather focal CNV calls; these common region of the overlapping CNV would be the new CONSENSUS CNV.
 
 11) **Sort and merge** the CNVs from the comparison pairs ,`manta-cnvkit` `manta-freec` `cnvkit-freec`, together into 1 file
 12) Resolve overlapping segments where duplications are embedded within larger deletion segments, or deletions within duplications.

analyses/copy_number_consensus_call/Snakefile

@@ -98,14 +98,13 @@ rule manta_filter:
         ## the first awk also filters out for CNV length
         ## The sort command sorts the first digit of chromosome number numerically
         ## The last pipe is to introduce tab into the file and output file name.        
-        """awk '$6~/DEL/ {{if ($5 > {params.SIZE_CUTOFF}) {{print "chr"$2,$3,$4,$5,"NA","NA","NA",$6}}}}' {input} """
+        """awk '$6~/DEL/ {{if ($5 > {params.SIZE_CUTOFF} && $11 == 'PASS') {{print "chr"$2,$3,$4,$5,"NA","NA","NA",$6}}}}' {input} """
         """ | sort -k1,1 -k2,2n """
         """ | tr [:blank:] '\t' > {output.manta_del} && """
-        """awk '$6~/DUP/ {{if ($5 > {params.SIZE_CUTOFF}) {{print "chr"$2,$3,$4,$5,"NA","NA","NA",$6}}}}' {input} """
+        """awk '$6~/DUP/ {{if ($5 > {params.SIZE_CUTOFF}  && $11 == 'PASS') {{print "chr"$2,$3,$4,$5,"NA","NA","NA",$6}}}}' {input} """
         """ | sort -k1,1 -k2,2n """
         """ | tr [:blank:] '\t' > {output.manta_dup}"""
 
-
 rule generate_excluded:
     # Combine the sets of regions that are not well called by CNV algorithms for exclusion
     input: