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].

  • Germline samples:
    • Single sample: Sentieon (bwa-mem) aligner & Sentieon DNAscope caller
    • Multi-sample: Sentieon (bwa-mem) aligner & Sentieon Haplotyper caller. Please see our article on joint calling.
  • Tumor/somatic samples: Sentieon (bwa-mem) aligner & Sentieon TNhaplotyper2 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.
  • DELLY: for whole-genome sequence (WGS) samples.

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