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Snakefile
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Snakefile
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rule gatk_filtermutectcalls:
input:
vcf="calls/snvs.vcf",
ref="genome.fasta",
output:
vcf="calls/snvs.mutect.filtered.vcf",
log:
"logs/gatk/filter/snvs.log",
params:
extra="--max-alt-allele-count 3", # optional arguments, see GATK docs
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"master/bio/gatk/filtermutectcalls"
rule gatk_filtermutectcalls_complete:
input:
vcf="calls/snvs.vcf",
ref="genome.fasta",
bam="mapped/a.bam",
intervals="intervals.bed",
# contamination="", # from gatk CalculateContamination
# segmentation="", # from gatk CalculateContamination
# f1r2="", # from gatk LearnReadOrientationBias
output:
vcf="calls/snvs.mutect.filtered.b.vcf",
log:
"logs/gatk/filter/snvs.log",
params:
extra="--max-alt-allele-count 3", # optional arguments, see GATK docs
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"master/bio/gatk/filtermutectcalls"