Snakemake workflow for annotating and filtering variant data

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vase_family_filtering_workflow
vase_family_filtering_workflow
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Snakemake workflow for annotating and filtering variant data in small families according to different inheritance patterns using VASE .

Code Snippets

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shell:
    "tabix -fp vcf {input} 2> {log}"
SnakeMake tabix From line 10 of rules/vase.smk 
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shell:
    "tabix -l {input[0]} > {output} 2> {log}"
SnakeMake tabix From line 24 of rules/vase.smk 
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shell:
    "tabix -fp vcf {input} 2> {log}"
SnakeMake tabix From line 37 of rules/vase.smk 
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shell:
    "bcftools view -O u {input.vcf} {wildcards.contig} | vase {params} -i - -o {output[0]} 2> {log}"
SnakeMake BCFtools From line 61 of rules/vase.smk 
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shell:
    "vase {params} -i {input.vcf} -o {output.vcf} 2> {log}"
SnakeMake From line 77 of rules/vase.smk 
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wrapper:
    "0.84.0/bio/picard/mergevcfs"
SnakeMake From line 93 of rules/vase.smk 
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wrapper:
  "0.84.0/bio/picard/mergevcfs"
SnakeMake From line 109 of rules/vase.smk 
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shell:
    "mv {input} {output} 2> {log}"
SnakeMake From line 122 of rules/vase.smk 
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shell:
    "vase_reporter {params} -o {wildcards.ext} {input} {output} 2> {log}"
SnakeMake From line 137 of rules/vase.smk 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


inputs = " ".join("INPUT={}".format(f) for f in snakemake.input.vcfs)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

shell(
    "picard"
    " MergeVcfs"
    " {java_opts}"
    " {extra}"
    " {inputs}"
    " OUTPUT={snakemake.output[0]}"
    " {log}"
)
Python Snakemake Picard snakemake-wrapper-utils From line 3 of mergevcfs/wrapper.py
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/david-a-parry/vase_family_filtering_workflow
Name: vase_family_filtering_workflow
Version: 1
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Copyright: Public Domain
License: None
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