Alignment and Calling

Overall description of VarSome's pipelines

VarSome Clinical uses Sentieon's implementation of bwa-mem for aligning reads to the genome. For variant calling, it uses Sentieon's variant caller [1] for samples sequenced using a capture kit and Astra Zeneca's VarDict [2] for those sequenced using amplicon kits.

  • Capture Kit
    • Germline samples:
      • Single-sample: Sentieon (bwa-mem) aligner & Sentieon DNAscope caller
    • Somatic samples:
      • Single-sample: Sentieon (bwa-mem) aligner & Sentieon TNhaplotyper2 caller.
      • Tumor/Normal: Sentieon (bwa-mem) aligner & Sentieon TNhaplotyper2 caller. 
  • Amplicon Kit:
    • Both somatic and germline amplicon kit samples use  Sentieon (bwa-mem) aligner & VarDict caller.

Default Workflow

  1. Adapter trimming is normally done before the FASTQ file is generated. The FASTQ files VarSome gets are therefore already trimmed.
  2. Read mapping
  3. Primer clipping (amplicon-based samples)
  4. Deduplication
  5. Indel realignment
  6. Base-quality recalibration
  7. Variant calling

CNV analysis

We use the alignments already created by Sentieon's implementation of bwa-mem. For CNV calling we use:

  • ExomeDepth: for targeted data such as whole-exome sequencing (WES) or gene panel samples and also for whole-genome sequencing (WGS) using multiple samples. 
  • DELLY: for a single whole-genome sequence (WGS) sample.

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