Overall description of VarSome's pipelines
- 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.
- Adapter trimming is normally done before the FASTQ file is generated. The FASTQ files VarSome gets are therefore already trimmed.
- Read mapping
- Primer clipping (amplicon-based samples)
- Indel realignment
- Base-quality recalibration
- Variant calling
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.