pipeline5 | pipeline first runs primary and secondary analysis | Genomics library

pipeline5 is a Java library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. pipeline5 has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

The pipeline first runs primary and secondary analysis on a reference (blood/normal) sample and tumor sample before comparing them in the final somatic pipeline. The GATK Haplotype caller is the final step of the single sample pipeline. Somatic pipelines continue with the tertiary analysis that is briefly described below. Under normal circumstances Pv5 starts with the input of one to n paired-end FASTQ files produced by a sequencing machine. The first task of the pipeline is to align these reads to the human reference genome (using the BWA algorithm). We use the largest core counts available and parallelise by sample (tumor/normal) and lane within each sample to achieve reasonable performance. Mark duplicates and sorting is performed after the per lane alignments with Sambamba. Various WGS metrics are collected via Picard tools for ad-hoc analysis and evaluation of automated QC in Health Checker. Samtools flag statistics are not consumed by any downstream stages, but useful in ad hoc QC and analysis. GATK's UnifiedGenotyper is used to call in 26 specific locations. The results are compared with a similar but separate DNA assay in Hartwig lab to rule out sample swaps. GATK's HaplotypeCaller is used to call germline variants on the reference sample only. These calls are not used in downstream algorithms but are the only genome-wide germline calls. Amber is an HMF in-house tool used to determine the minor allele copy number of heterozygous germline variants in the tumor sample. Cobalt is an HMF in-house tool used to determine read depth ratios. SAGE is an HMF in-house tool used to call somatic variants (MNVs, SNVs and Indels) between the tumor/reference pair. SAGE Germline is an HMF in-house tool used to call germline variants (MNVs, SNVs and Indels) in the reference sample. SAGE germline annotates all germline variants with their status in the tumor sample. GRIDSS is used to call structural variants between the tumor/reference pair. GRIPSS is an HMF in-house tool used to extract the somatic variants from the full structural variant call set from GRIDSS and remove all low quality calls. Purple is an HMF in-house tool which combines the read-depth ratios from Cobalt, BAFs from Amber, and structural/somatic variants to produce a comprehensive tumor analysis regarding purity, ploidy, drivers and annotated variants. Linx is an HMF in-house tool which interprets structural variants from Purple and calls fusions and homozygously disrupted genes. PEACH is an HMF in-house tool which matches SAGE germline calls with pharmacogenetic evidence. VIRUSBreakend is a module within GRIDSS that is used to determine viral presence in the tumor sample. Cuppa is an HMF in-house tool which tries to predict the primary tumor location based on the LINX and Purple results. CHORD is an external tool which evaluates whether the tumor is HR-deficient based on the complete set of variants found. PROTECT is an HMF in-house tool which annotates all drivers with their clinical relevance and decides on treatment and trial eligibility. Health Checker is an HMF in-house doing a final QC based off the purple results and WGS metrics.