SLUPipe’s variant callers by default run GDC Guideline arguments. However, each variant caller can be customized to tailor to a user’s need. This is accomplished by providing a JSON file during SLUPipe’s execution:
$ python3 slupipe.py config.json <muse.json> <mutect.json> <varscan.json> <sniper.json> ...
Please Note: You’re not required to provide a JSON file for variant callers you don’t intend to run custom arguments. SLUPipe will keep running those variant callers using the GDC configuration.
Creating Custom Variant Caller JSON Files
The JSON files must abide to the following formats. In addition, arguments provided must exist for the variant caller. Consult the manuals of the variant caller for further information.
Muse:
[
{
"call": {
"-f": "./referenceFiles/Homo_sapiens_assembly38.fasta",
"-r": "chr1:16,000,000-215,000,000",
"-O": "./muse_output/"
},
"sump": {
"-I": "./muse_output/muse_call.MuSE.txt",
"-E": "",
"-D": "./referenceFiles/dbSNP142_GRCh38_subset50k.vcf.gz",
"-O": "./muse_output/"
}
}
]
IMPORTANT: Name config file “muse.json” otherwise SLUPipe won’t detect it.
Mutect:
[
{
"mutect2": {
"-nct": "8"
}
}
]
IMPORTANT: Name config file “mutect.json” otherwise SLUPipe won’t detect it.
Varscan: [ {
"samtools": {
"-q": "1"
},
"varscan_somatic": {
"--mpileup": "1",
"--min-coverage": "8",
"--min-coverage-normal": "8",
"--min-coverage-tumor": "6",
"--min-var-freq": "0.10",
"--min-freq-for-hom":"0.75",
"--normal-purity": "1.0",
"--tumor-purity":"1.00",
"--p-value": "0.99",
"--somatic-p-value":"0.05",
"--strand-filter": "0"
},
"varscan_processSomatic": {
"--min-tumor-freq": "0.10",
"--max-normal-freq": "0.05",
"--p-value": "0.07"
}
}
]
IMPORTANT: Name config file “varscan.json” otherwise SLUPipe won’t detect it.
Bam Somatic Sniper:
[
{
"bam_somatic_sniper": {
"-q": "1",
"-L": "-G",
"-Q": "15",
"-s": "0.01",
"-T": "0.85",
"-N": "2",
"-r": "0.001",
"-n": "NORMAL",
"-t": "TUMOR",
"-F": "vcf"
}
}
]
IMPORTANT: Name config file “sniper.json” otherwise SLUPipe won’t detect it.
Strelka 2
[
{
"strelka_config": {
"--outputCallableRegions": "",
"--exome": ""
},
"strelka_run": {
"-m": "local",
"-j": "4"
}
}
]
IMPORTANT: Name config file “strelka.json” otherwise SLUPipe won’t detect it.
Pindel:
[
{
"pindel_read": {
"-T": "4"
},
"pindel2vcf": {
"-R": "Homo_Sapiens_Assembly38",
"-d": "20101123"
}
}
]
IMPORTANT: Name config file “strelka.json” otherwise SLUPipe won’t detect it.
Platypus:
[
{
"call_Variants": {
"--nCPU=": "4"
}
}
]
IMPORTANT: Name config file “platypus.json” otherwise SLUPipe won’t detect it.