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# System prepended metadata

title: Autoseq Targeted Variant Calling

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# Autoseq Targeted Variant Calling

## Small Nuleotide Variants (SNVs) Caller

### Somatic Variant Callers 

* GATK4 - Mutect2
* VarDict
* Varscan
* Strelka

somatic VCF merging - SomaticSeq 
**somatic vcf file:** $clinseq_barcodes.all.somatic.vep.vcf

#### Filters Applied

Include a variant, if 
- the filter colum has PASS or LowQual tag (and)
- VEP Impact ann is either HIGH or MODERATE or **Is_splice_region_variant**


### Germline Variant Callers

- GATK4 - HaplotypeCaller
- Strelka Germline

Germline vcf merging: GATK3 CombineVariants 

**Germline vcf file:** $normal_barcode.all.germline.vep.vcf

#### Filters Applied

Include a variant, if 
- the filter colum has only PASS (and)
- VEP Impact ann is either HIGH or MODERATE or **Is_splice_region_variant** (and)
- the variant is called by both or haplotypecaller 

 Exclude variants, if
 - VEP **impact is LOW or MODERATE** and not pathogenic in clinvar annotation


## Structural Variant Callers

#### svcaller (in-house tool)

GTF files for each event (INV, DUP, DEL, TRA)
