Introduction
This is the implementation of KhanLab NGS Pipeline using Snakemake.
Installation
The easiest way to get this pipeline is to clone the repository.
git clone https://github.com/patidarr/ngs_pipeline.git
This pipeline is available on NIH biowulf cluster, contact me if you would like to do a test run. The data from this pipeline could directly be ported in OncoGenomics-DB, an application created to visualize NGS data available to NIH users.
Requirements
mutt
gnu parallel
SLURM or PBS for resource management
Bioinformatics Tools Listed in config files
Following R Packages
Conventions
- Sample names cannot have “/” or “.” in them
- Fastq files end in “.fastq.gz”
- Fastq files are stored in DATA_DIR (Set as Environment Variable)
DNASeq:
- QC
- BWA, Novoalign
- Broad Standard Practices on bwa bam
- Haplotype Caller, Platupys, Bam2MPG, MuTect, Strelka
- snpEff, Annovar, SIFT, pph2, Custom Annotation
- Coverage Plot, Circos Plot, Hotspot Coverage Box Plot
- Create input format for oncogenomics database (Patient Level)
- Make Actionable Classification for Germline and Somatic Mutations
- Copy number based on the simple T/N LogRatio (N cov >=30), Corrected for Total # Reads
- Copy number, tumor purity using sequenza
- LRR adjusted to center
- Contamination using conpair
- HLA Typing
- Neoantigen Prediction
- pVAC-Seq
methods: NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign
epitope length: 8,9,10,11
RNASeq:
- QC
- Tophat, STAR
- Broad Standard Practices on STAR bam
- fusion-catcher, tophat-fusion, deFuse
- Cufflinks (ENS and UCSC)
- Rsubread TPM (ENS, UCSC), Gene, Transcript and Exon Level
- In-house Exon Expression (ENS and UCSC)
- Haplotype Caller
- snpEff, Annovar, SIFT, pph2, Custom Annotation
- Actionable Fusion classification
Patient:
- Genotyping On Patient.
1000g sites are evaluated for every library and then compared (all vs all)
If two libraries come from a patient the match should be pretty good >80%
- Still to develop:
If the match is below a certain threshold, break the pipeline for patient.
Rulegraph
DAG for example Sample
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