Overall description of VarSome's pipelines
- Sentieon: Sentieon (bwa-mem) aligner & Sentieon caller
- Tumor/somatic samples: Sentieon (bwa-mem) aligner & Sentieon TNscope caller (see below)
- 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).
- Read mapping
- Indel realignment
- Base-quality recalibration
- Variant calling
Please see our article on joint calling.