Tools¶
This table lists information about the steps performed, tools used, and their details.
Module | Category | Analysis Type | Software | Version | Rule File(s) |
Preprocessing | Preprocessing | trim | Trimmomatic | 0.39 | trim_map_preprocess.smk |
map | bwa | 0.7.17 | trim_map_preprocess.smk | ||
markdup | samblaster | 0.1.25 | trim_map_preprocess.smk | ||
GATK4 Best Practices | GATK4 | 4.2.2 | |||
SNP/Indel Calling | Mutect2 | GATK 4.2.2 | somatic_snps.paired.smk, somatic_snps.tumor_only.smk | ||
Strelka | 2.9.0 | somatic_snps.paired.smk | |||
VarScan | 2.4.3 | somatic_snps.paired.smk, somatic_snps.tumor_only.smk | |||
Mutect | 1.1.7 | somatic_snps.paired.smk, somatic_snps.tumor_only.smk | |||
VarDict | 1.4 | somatic_snps.paired.smk, somatic_snps.tumor_only.smk | |||
FFPE Artifact Filter | SOBDetector | 1.0.4 | ffpe.smk | ||
Consensus SNP/Indels | GATK3 CombineVariants | GATK_3.8-1 | somatic_snps.common.smk | ||
Somatic Copy Number Variation (CNV) | CNV | Control-FREEC | 11.5 | somatic_snps.paired.smk | |
Sequenza | somatic_snps.paired.smk | ||||
Somatic Analysis | Annotate | vcf2maf | somatic_snps.common.smk | ||
Germline | Germline SNV Calling | Germline Variants | HaplotypeCaller | GATK_4.2.2 | germline.smk |
Germline Analysis | Ancestry | Somalier | qc.smk | ||
Relatedness | Somalier | qc.smk | |||
QC Metrics | QC | depth | qualimap | 2.2.1 | qc.smk |
report | multiqc | 1.11 | qc.smk | ||
base quality | FastQC | 0.11.9 | qc.smk | ||
contamination | Fastq Screen | 0.14.1 | qc.smk | ||
kraken | 2.1.2 | qc.smk | |||
variant quality | vcftools stat | 0.1.16 | qc.smk | ||
bcftools_stat | 1.9 | qc.smk | |||
variant effect | SNPeff | 4.3t | qc.smk | ||
General | General | R scripts | R | 4.1 | general |
variant wrangling | bcftools | 1.9 | general | ||
vcftools | 0.1.16 | general | |||
alignment wrangling | samtools | 1.8 | general | ||
Orchestration | Orchestration | Containerization | singularity | 3.8.5 | Orchestration |
Workflow managemanet | snakemake | 6.8.2 | Orchestration |