Alignment and Calling

Overall description of VarSome's pipelines

VarSome Clinical uses Sentieon's implementation of bwa-mem for aligning reads to the genome and Sentieon's implementation of GATK for variant calling [1].

  • Sentieon: Sentieon (bwa-mem) aligner & Sentieon caller
  • Tumor/somatic samples: Sentieon (bwa-mem) aligner & Sentieon TNscope caller (see below)

Default Workflow

  1. Adapter trimming is normally done before the FASTQ file is generated. The FASTQ files VarSome gets are therefore already trimmed. Low quality bases are ignored by the variant caller (soft clipping).
  2. Read mapping
  3. Indel realignment
  4. Base-quality recalibration
  5. Variant calling

Joint calling

Please see our article on joint calling.

Tumor Samples

 We use Sentieon's TNscope tool for both matched tumor-normal pairs and single tumor samples.

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