SLUPipe: A (S)omatic Ana(L)ysis (U)mbrella (Pipe)line

SLUPipe is a DNA Sequencing Variant Calling Pipeline based on the National Cancer Institute’s GDC guidelines. SLUPipe focuses towards automating, merging and parallelizing the following GDC’s DNA-Sequence Analysis workflows to increase sample analysis throughput :

• Somatic Variant Calling
• Variant Annotation
• Aggregated Somatic Mutation

For further information on GDC Guidelines visit: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

Features

SLUPipe provides variant calling for paired (Normal & Tumor) and non-paired (Tumor Only) aligned samples at the request of the research group:

Variant Callers

Paired Sample Variant Callers (Normal Mode):

• MuSE (1.0.rc)
• Mutect2 (GATK3.8.1)
• Somatic Sniper (1.0.5.0)
• Varscan (2.4.3.2)
• Strelka 2 (2.9.10)

Non-paired Sample Variant Callers (Tumor Only):

• Pindel (0.2.5b9)
• Platypus (1.0.3)
• Mutect2

Variants callers can be toggled on/off as requested by the user (config file).

Variant Annotation

Raw VCF files are annotated using Ensembl VEP (v95). The following databases are used for VCF Annotation:

• GENCODE v.22
• sift v.5.2.2
• ESP v.20141103
• polyphen v.2.2.2
• dbSNP v.146
• Ensembl genebuild v.2014-07
• Ensembl regbuild v.13.0
• HGMD public v.20154
• ClinVar v.201601