def constructor(self):
self.input("bam", BamBai)
self.input("reference", FastaWithDict)
# optional
self.input("intervals", BedTabix(optional=True))
self.input("is_exome", Boolean(optional=True))
self.input("manta_config", File(optional=True))
self.input("strelka_config", File(optional=True))
self.step(
"manta",
Manta_1_5_0(
bam=self.bam,
reference=self.reference,
callRegions=self.intervals,
exome=self.is_exome,
config=self.manta_config,
),
)
self.step(
"strelka",
StrelkaGermline_2_9_10(
bam=self.bam,
reference=self.reference,
callRegions=self.intervals,
exome=self.is_exome,
config=self.strelka_config,
),
)
# normalise and filter "PASS" variants
self.step(
"splitnormalisevcf",
SplitMultiAllele(
vcf=self.strelka.variants.as_type(CompressedVcf),
reference=self.reference,
),
)
self.step(
"filterpass",
VcfToolsvcftoolsLatest(
vcf=self.splitnormalisevcf.out,
removeFileteredAll=True,
recode=True,
recodeINFOAll=True,
),
)
self.output("sv", source=self.manta.diploidSV)
self.output("variants", source=self.strelka.variants)
self.output("out", source=self.filterpass.out)
def constructor(self):
self.input("bam", BamBai)
self.input("reference", FastaWithDict)
self.input("intervals", BedTabix(optional=True))
self.input("is_exome", Boolean(optional=True))
self.step(
"manta",
Manta_1_5_0(
bam=self.bam,
reference=self.reference,
callRegions=self.intervals,
exome=self.is_exome,
),
)
self.step(
"strelka",
StrelkaGermline_2_9_10(
bam=self.bam,
reference=self.reference,
indelCandidates=self.manta.candidateSmallIndels,
callRegions=self.intervals,
exome=self.is_exome,
),
)
self.step(
"bcfview",
BcfToolsView_1_5(file=self.strelka.variants,
applyFilters=["PASS"]),
)
self.step(
"split_multi_allele",
SplitMultiAllele(vcf=self.bcfview.out, reference=self.reference),
)
self.output("diploid", source=self.manta.diploidSV)
self.output("variants", source=self.strelka.variants)
self.output("out", source=self.split_multi_allele.out)
def constructor(self):
self.input("normal_bam", BamBai)
self.input("tumor_bam", BamBai)
self.input("reference", FastaWithDict)
# optional
self.input("intervals", BedTabix(optional=True))
self.input("is_exome", Boolean(optional=True))
self.input("manta_config", File(optional=True))
self.input("strelka_config", File(optional=True))
self.step(
"manta",
Manta_1_5_0(
bam=self.normal_bam,
tumorBam=self.tumor_bam,
reference=self.reference,
callRegions=self.intervals,
exome=self.is_exome,
config=self.manta_config,
),
)
self.step(
"strelka",
StrelkaSomatic_2_9_10(
indelCandidates=self.manta.candidateSmallIndels,
normalBam=self.normal_bam,
tumorBam=self.tumor_bam,
reference=self.reference,
callRegions=self.intervals,
exome=self.is_exome,
config=self.strelka_config,
),
)
self.step(
"concatvcf",
ConcatStrelkaSomaticVcf(
headerVcfs=[self.strelka.snvs, self.strelka.indels],
contentVcfs=[self.strelka.snvs, self.strelka.indels],
),
)
self.step("sortvcf", BcfToolsSort_1_9(vcf=self.concatvcf.out))
self.step(
"splitnormalisevcf",
SplitMultiAllele(vcf=self.sortvcf.out, reference=self.reference),
)
self.step(
"extractaddp",
ExtractStrelkaSomaticADDP_0_1_1(vcf=self.splitnormalisevcf.out),
)
self.step(
"filterpass",
VcfToolsvcftoolsLatest(
vcf=self.extractaddp.out,
removeFileteredAll=True,
recode=True,
recodeINFOAll=True,
),
)
self.output("tumor_sv", source=self.manta.somaticSV)
self.output("normal_sv", source=self.manta.diploidSV)
self.output("variants", source=self.sortvcf.out)
self.output("out", source=self.filterpass.out)