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Switch to tabs for filter output #2

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merged 2 commits into from
Dec 17, 2019
Merged

Switch to tabs for filter output #2

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e2090be
Switch to tabs for filter output
jashapiro Dec 16, 2019
f4978e2
Add "chr" to output files that don't have them
jashapiro Dec 16, 2019
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33 changes: 19 additions & 14 deletions analyses/copy_number_consensus_call/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,10 @@
# Updated Dec 5, 2019

## Define the ending file(s) that we want
ALL_FREEC= expand("../../scratch/interim/{sample}.freec.dup.filtered.bed", sample=config["samples"])
ALL_CNVKIT= expand("../../scratch/interim/{sample}.cnvkit.dup.filtered.bed", sample=config["samples"])
OUTPUT= expand("../../scratch/interim/{sample}.{caller}.dup.filtered.bed",
OUTPUT= expand("../../scratch/interim/{sample}.{caller}.{dupdel}.filtered.bed",
sample=config["samples"],
caller=["freec", "cnvkit", "manta"])
caller=["freec", "cnvkit", "manta"],
dupdel=["dup", "del"])


## Define the first rule of the Snakefile. This rule determines what the final file is and which steps to be taken.
Expand Down Expand Up @@ -35,12 +34,14 @@ rule freec_filter:
## The first awk looks at column 6 to filter out for loss/gain. Then it prints out 6 of the 7 columns above
## The pipe into the second awk filters the CNV length, freec pval, and add in the CNV type
## The last pipe is to sort first digit of chromosome number numerically
"""awk '$6~/loss/ {{print $2,$3,$4,($4-$3 + 1),$5,$9}}' {input.events} """
"""awk '$6~/loss/ {{print "chr"$2,$3,$4,($4-$3 + 1),$5,$9}}' {input.events} """
""" | awk '{{if ($4 > {params.SIZE_CUTOFF} && $6 < {params.FREEC_PVAL}){{print $0,"DEL"}}}}' """
""" | sort -k1,1 -k2,2n > {output.freec_del} && """
"""awk '$6~/gain/ {{print $2,$3,$4,($4-$3 + 1),$5,$9}}' {input.events} """
""" | sort -k1,1 -k2,2n """
""" | tr [:blank:] '\t' > {output.freec_del} && """
"""awk '$6~/gain/ {{print "chr"$2,$3,$4,($4-$3 + 1),$5,$9}}' {input.events} """
""" | awk '{{if ($4 > {params.SIZE_CUTOFF} && $6 < {params.FREEC_PVAL}){{print $0,"DUP"}}}}' """
""" | sort -k1,1 -k2,2n > {output.freec_dup}"""
""" | sort -k1,1 -k2,2n """
""" | tr [:blank:] '\t' > {output.freec_dup}"""

rule cnvkit_filter:
input:
Expand All @@ -60,10 +61,12 @@ rule cnvkit_filter:
## The last pipe is to sort first digit of chromosome number numerically
"""awk '$7<2 {{print $2,$3,$4,($4-$3 + 1),$7,"NA"}}' {input.events} """
""" | awk '{{if ($4 > {params.SIZE_CUTOFF}){{print $0,"DEL"}}}}' """
""" | sort -k1,1 -k2,2n > {output.cnvkit_del} && """
""" | sort -k1,1 -k2,2n """
""" | tr [:blank:] '\t' > {output.cnvkit_del} && """
"""awk '$7>2 {{print $2,$3,$4,($4-$3 + 1),$7,"NA"}}' {input.events} """
""" | awk '{{if ($4 > {params.SIZE_CUTOFF}){{print $0,"DUP"}}}}' """
""" | sort -k1,1 -k2,2n > {output.cnvkit_dup}"""
""" | sort -k1,1 -k2,2n """
""" | tr [:blank:] '\t' > {output.cnvkit_dup}"""

rule manta_filter:
input:
Expand All @@ -81,10 +84,12 @@ rule manta_filter:
## The first awk looks at column 6 to filter out for loss/gain (DEL/DUP). Then it prints out 6 of the 7 columns above. Put NA for both p-value and copy number since MANTA results don't have these values.
## the first awk also filters out for CNV length
## The last pipe is to sort first digit of chromosome number numerically
"""awk '$6~/DEL/ {{if ($5 > {params.SIZE_CUTOFF}) {{print$2,$3,$4,$5,"NA","NA",$6}}}}' {input} """
""" | sort -k1,1 -k2,2n > {output.manta_del} && """
"""awk '$6~/DUP/ {{if ($5 > {params.SIZE_CUTOFF}) {{print$2,$3,$4,$5,"NA","NA",$6}}}}' {input} """
""" | sort -k1,1 -k2,2n > {output.manta_dup}"""
"""awk '$6~/DEL/ {{if ($5 > {params.SIZE_CUTOFF}) {{print "chr"$2,$3,$4,$5,"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",$6}}}}' {input} """
""" | sort -k1,1 -k2,2n """
""" | tr [:blank:] '\t' > {output.manta_dup}"""


rule filter_telomeres:
Expand Down