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mutect2.snakefile
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mutect2.snakefile
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configfile: "config/samples.yaml"
configfile: "config/config.yaml"
m2_extra_args=config["m2_extra_args"]
rule all:
input:
expand("results/mutect2/{tumor}/unfiltered_{chromosomes}.vcf.gz",tumor=config["normals"],chromosomes=config["chromosomes"]),
expand("results/mutect2/{tumor}/unfiltered_{chromosomes}.vcf.gz.tbi",tumor=config["normals"],chromosomes=config["chromosomes"]),
expand("results/mutect2/{tumor}/unfiltered_{chromosomes}_f1r2.tar.gz",tumor=config["normals"],chromosomes=config["chromosomes"]),
expand("results/mutect2/{tumor}/unfiltered_{chromosomes}.vcf.gz.stats",tumor=config["normals"],chromosomes=config["chromosomes"]),
expand("results/mutect2/{tumor}/{tumor}_{chromosomes}_bamout.bai",tumor=config["normals"],chromosomes=config["chromosomes"]),
expand("results/mutect2/{tumor}/{tumor}_{chromosomes}_bamout.bam",tumor=config["normals"],chromosomes=config["chromosomes"]),
expand("results/MergeMutectStats/{tumor}/mutect_merged.stats",tumor=config["normals"]),
expand("results/GatherVcfs/{tumor}/gathered_unfiltered.vcf.gz",tumor=config["normals"]),
expand("results/LearnReadOrientationModel/{tumor}/read_orientation_model.tar.gz", tumor = config["normals"]),
expand("results/GatherVcfs/{tumor}/gathered_unfiltered.vcf.gz.tbi", tumor = config["normals"])
if m2_extra_args == True:
rule mutect2:
input:
tumor_filepath = lambda wildcards: config["base_file_name"][wildcards.tumor],
norm_filepath=lambda wildcards: config["base_file_name"][config["normals"][wildcards.tumor]]
output:
vcf = temp("results/mutect2/{tumor}/unfiltered_{chromosomes}.vcf.gz"),
tbi = temp("results/mutect2/{tumor}/unfiltered_{chromosomes}.vcf.gz.tbi"),
tar = temp("results/mutect2/{tumor}/unfiltered_{chromosomes}_f1r2.tar.gz"),
stats = temp("results/mutect2/{tumor}/unfiltered_{chromosomes}.vcf.gz.stats"),
bam = "results/mutect2/{tumor}/{tumor}_{chromosomes}_bamout.bam",
bai = "results/mutect2/{tumor}/{tumor}_{chromosomes}_bamout.bai"
params:
reference_genome = config["reference_genome"],
germline_resource = config["germline_resource"],
gatk = config["gatk_path"],
panel_of_normals = config["panel_of_normals"],
normals = lambda wildcards: config["normals"][wildcards.tumor]
log:
"logs/mutect2/{tumor}_{chromosomes}_mutect2.txt"
shell:
"({params.gatk} Mutect2 \
-reference {params.reference_genome} \
-input {input.tumor_filepath} \
-input {input.norm_filepath} \
-normal {params.normals} \
-intervals {wildcards.chromosomes} \
--germline-resource {params.germline_resource} \
--f1r2-tar-gz {output.tar} \
--panel-of-normals {params.panel_of_normals} \
--read-filter PassesVendorQualityCheckReadFilter \
--read-filter HasReadGroupReadFilter \
--read-filter NotDuplicateReadFilter \
--read-filter MappingQualityAvailableReadFilter \
--read-filter MappingQualityReadFilter \
--minimum-mapping-quality 30 \
--read-filter OverclippedReadFilter \
--filter-too-short 25 \
--read-filter GoodCigarReadFilter \
--read-filter AmbiguousBaseReadFilter \
--native-pair-hmm-threads 2 \
--seconds-between-progress-updates 100 \
--downsampling-stride 20 \
--max-reads-per-alignment-start 6 \
--max-suspicious-reads-per-alignment-start 6 \
--bam-output {output.bam} \
-output {output.vcf}) 2> {log}"
else:
rule mutect2:
input:
tumor_filepath = lambda wildcards: config["base_file_name"][wildcards.tumor],
norm_filepath=lambda wildcards: config["base_file_name"][config["normals"][wildcards.tumor]]
output:
vcf = temp("results/mutect2/{base_file_name}/unfiltered_{chromosomes}.vcf.gz"),
tbi = temp("results/mutect2/{base_file_name}/unfiltered_{chromosomes}.vcf.gz.tbi"),
tar = temp("results/mutect2/{base_file_name}/unfiltered_{chromosomes}_f1r2.tar.gz"),
stats = temp("results/mutect2/{base_file_name}/unfiltered_{chromosomes}.vcf.gz.stats"),
bam = "results/mutect2/{tumor}/{tumor}_{chromosomes}_bamout.bam",
bai = "results/mutect2/{tumor}/{tumor}_{chromosomes}_bamout.bai"
params:
reference_genome = config["reference_genome"],
germline_resource = config["germline_resource"],
gatk = config["gatk_path"],
panel_of_normals = config["panel_of_normals"],
normals = lambda wildcards: config["normals"][wildcards.tumor]
log:
"logs/mutect2/{base_file_name}_{chromosomes}_mutect2.txt"
shell:
"({params.gatk} Mutect2 \
-reference {params.reference_genome} \
-input {input.tumor_filepath} \
-input {input.norm_filepath} \
-normal {params.normals} \
-intervals {wildcards.chromosomes} \
--germline-resource {params.germline_resource} \
--f1r2-tar-gz {output.tar} \
--panel-of-normals {params.panel_of_normals} \
--bam-output {output.bam} \
-output {output.vcf}) 2> {log}"
rule MergeMutectStats:
output:
"results/MergeMutectStats/{tumor}/mutect_merged.stats"
params:
gatk = config["gatk_path"],
chromosomes=config["chromosomes"]
log:
"logs/MergeMutectStats/{tumor}_merge_mutect_stats.txt"
shell:
"""
all_stat_inputs=`for chrom in {params.chromosomes}; do
printf -- "-stats results/mutect2/{wildcards.tumor}/unfiltered_$chrom.vcf.gz.stats "; done`
({params.gatk} MergeMutectStats \
$all_stat_inputs \
-O {output}) 2> {log}"""
rule GatherVcfs:
output:
"results/GatherVcfs/{base_file_name}/gathered_unfiltered.vcf.gz"
params:
java = config["java"],
picard_jar = config["picard_jar"],
chromosomes=config["chromosomes"]
log:
shell:
"""
all_vcf_inputs=`for chrom in {params.chromosomes}; do
printf -- "I=results/mutect2/{wildcards.base_file_name}/unfiltered_$chrom.vcf.gz "; done`
({params.java} -jar {params.picard_jar} GatherVcfs \
$all_vcf_inputs \
O={output}) 2> {log}"""
rule LearnReadOrientationModel:
input:
chr1_tar = "results/mutect2/{base_file_name}/unfiltered_chr1_f1r2.tar.gz",
chr2_tar = "results/mutect2/{base_file_name}/unfiltered_chr2_f1r2.tar.gz",
chr3_tar = "results/mutect2/{base_file_name}/unfiltered_chr3_f1r2.tar.gz",
chr4_tar = "results/mutect2/{base_file_name}/unfiltered_chr4_f1r2.tar.gz",
chr5_tar = "results/mutect2/{base_file_name}/unfiltered_chr5_f1r2.tar.gz",
chr6_tar = "results/mutect2/{base_file_name}/unfiltered_chr6_f1r2.tar.gz",
chr7_tar = "results/mutect2/{base_file_name}/unfiltered_chr7_f1r2.tar.gz",
chr8_tar = "results/mutect2/{base_file_name}/unfiltered_chr8_f1r2.tar.gz",
chr9_tar = "results/mutect2/{base_file_name}/unfiltered_chr9_f1r2.tar.gz",
chr10_tar = "results/mutect2/{base_file_name}/unfiltered_chr10_f1r2.tar.gz",
chr11_tar = "results/mutect2/{base_file_name}/unfiltered_chr11_f1r2.tar.gz",
chr12_tar = "results/mutect2/{base_file_name}/unfiltered_chr12_f1r2.tar.gz",
chr13_tar = "results/mutect2/{base_file_name}/unfiltered_chr13_f1r2.tar.gz",
chr14_tar = "results/mutect2/{base_file_name}/unfiltered_chr14_f1r2.tar.gz",
chr15_tar = "results/mutect2/{base_file_name}/unfiltered_chr15_f1r2.tar.gz",
chr16_tar = "results/mutect2/{base_file_name}/unfiltered_chr16_f1r2.tar.gz",
chr17_tar = "results/mutect2/{base_file_name}/unfiltered_chr17_f1r2.tar.gz",
chr18_tar = "results/mutect2/{base_file_name}/unfiltered_chr18_f1r2.tar.gz",
chr19_tar = "results/mutect2/{base_file_name}/unfiltered_chr19_f1r2.tar.gz",
chr20_tar = "results/mutect2/{base_file_name}/unfiltered_chr20_f1r2.tar.gz",
chr21_tar = "results/mutect2/{base_file_name}/unfiltered_chr21_f1r2.tar.gz",
chr22_tar = "results/mutect2/{base_file_name}/unfiltered_chr22_f1r2.tar.gz",
chrX_tar = "results/mutect2/{base_file_name}/unfiltered_chrX_f1r2.tar.gz"
output:
"results/LearnReadOrientationModel/{base_file_name}/read_orientation_model.tar.gz"
params:
gatk = config["gatk_path"]
log:
"logs/learn_read_orientation_model/{base_file_name}_learn_read_orientation_model.txt"
shell:
"({params.gatk} LearnReadOrientationModel \
-I {input.chr1_tar} \
-I {input.chr2_tar} \
-I {input.chr3_tar} \
-I {input.chr4_tar} \
-I {input.chr5_tar} \
-I {input.chr6_tar} \
-I {input.chr7_tar} \
-I {input.chr8_tar} \
-I {input.chr9_tar} \
-I {input.chr10_tar} \
-I {input.chr11_tar} \
-I {input.chr12_tar} \
-I {input.chr13_tar} \
-I {input.chr14_tar} \
-I {input.chr15_tar} \
-I {input.chr16_tar} \
-I {input.chr17_tar} \
-I {input.chr18_tar} \
-I {input.chr19_tar} \
-I {input.chr20_tar} \
-I {input.chr21_tar} \
-I {input.chr22_tar} \
-I {input.chrX_tar} \
-O {output}) 2> {log}"
rule IndexFeatureFile:
input:
vcf = "results/GatherVcfs/{base_file_name}/gathered_unfiltered.vcf.gz"
output:
"results/GatherVcfs/{base_file_name}/gathered_unfiltered.vcf.gz.tbi"
params:
gatk = config["gatk_path"]
log:
"logs/IndexFeatureFile/{base_file_name}.log"
shell:
"({params.gatk} IndexFeatureFile \
-I {input.vcf} \
-O {output}) 2> {log}"