---
title: Alignment and Calling
description: Overall description of VarSome's pipelines
---
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# Alignment and Calling
## Overall description of VarSome's pipelines
*[VarSome Clinical](https://landing.varsome.com/varsome-clinical?hsLang=en)* uses Sentieon's implementation of *bwa-mem* for aligning reads to the genome. For variant calling, it uses Sentieon's variant caller \[[1](https://www.frontiersin.org/articles/10.3389/fgene.2019.00736/full)\] for samples sequenced using a capture kit and Astra Zeneca's VarDict \[[2](https://github.com/AstraZeneca-NGS/VarDictJava)\] for those sequenced using amplicon kits.
- **Capture Kit**
- **Germline samples**:
- Single-sample: Sentieon (*bwa-mem*) aligner & Sentieon *DNAscope* caller
- - - Multi-sample: Sentieon (bwa-mem) aligner & Sentieon *DNAscope* caller. Please see [our article on joint calling](https://docs.varsome.com/en/joint-calling?hsLang=en).
- **Somatic samples:**
- Single-sample: Sentieon (*bwa-mem*) aligner & Sentieon *TNhaplotyper2* caller.
- Tumor/Normal: Sentieon (*bwa-mem*) aligner & Sentieon *TNhaplotyper2*caller.
- **Amplicon Kit:**
- Both somatic and germline amplicon kit samples use Sentieon (bwa-mem) aligner & *VarDict* 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. Base-quality recalibration
6. Variant calling
### CNV analysis
We use the alignments already created by Sentieon's implementation of *bwa-mem*. For CNV calling we use:
- [ExomeDepth](https://pubmed.ncbi.nlm.nih.gov/22942019/): for targeted data such as whole-exome sequencing (WES) or gene panel samples and also for whole-genome sequencing (WGS) using multiple samples.
- [DELLY](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436805/): for a single whole-genome sequence (WGS) sample.
### Related articles
- [Can you explain what "Call status" is?](https://docs.saphetor.com/what-is-call-status?hsLang=en)
- [Targeted/Untargeted Calling on VarSome Clinical](https://docs.varsome.com/en/targeted-calling-on-varsome-clinical?hsLang=en)
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