Overall description of VarSome's pipelines
- Sentieon: Sentieon (bwa-mem) aligner & Sentieon DNAscope caller
- Tumor/somatic samples: Sentieon (bwa-mem) aligner & Sentieon TNhaplotyper2 caller (see below)
- Adapter trimming is normally done before the FASTQ file is generated. The FASTQ files VarSome gets are therefore already trimmed.
- Read mapping
- Primer clipping
- Indel realignment
- Base-quality recalibration
- Variant calling
Please see our article on joint calling.