Overview

  • Quality Control

    Raw sequencing reads are assessed for quality issues that may lead to inaccurate results

  • Pre-processing

    • Remove sequencing adapters if they are present in any reads
    • Merge overlapping 3' regions for paired-end mates, reducing the potential for false positive variant calls

  • Alignment

    Align reads to the reference genome using any combination of the following:

    * requires a license for multi-threaded mode

  • Alignment Refinement

    • Filter low quality alignments
    • Remove PCR duplicates
    • Realign around InDel regions
    • Recalibrate base quality scores

  • Variant Calling and Filtering

    Germline variant callers:

    GATK HaplotypeCaller, GATK UnifiedGenotyper, FreeBayes, SAMtools mpileup/bcftools, Issac Variant Caller

    Somatic variant callers:

    MuTect, Shimmer, SomaticSniper, Strelka, VarScan2, Virmid

    Customized filtration for high-confident calls

  • Variant Annotation

    Gene symbol, amino acid changes, genomic features, CADD, COSMIC, clinical significance, deleterious prediction, population allele frequency, etc.

  • Report Generation

    • Interactive exploration of raw read quality, alignment metrics, and integrated variants sets
    • Dynamic search and filtration by gene symbol, population frequency, variant set concordance
    • Assist in downstream customization of potential disease-causing mutations
    • Stand-alone RShiny tool for desktop visualization