GATK4 Processes
This section contains processes related to GATK4 variant calling.
| Process | Description |
|---|---|
| Add Or Replace Read Groups | Add or replace read groups |
| Analyze Covariates | Analyze covariates |
| AnalyzeCovariates | Analyze covariates (variant) |
| Apply BSQRS | Apply base quality score recalibration |
| Base Recalibration | Base quality recalibration |
| BaseRecalibrator | Base recalibrator |
| BQSR | Base quality score recalibration |
| Build GATK4 Genome Dictionary | Build genome dictionary |
| BWA Align | BWA alignment |
| Get Metrics | Get alignment metrics |
| HaplotypeCaller | GATK HaplotypeCaller |
| Mark Duplicates | Mark duplicate reads |
| Mutect2 | GATK Mutect2 somatic caller |
| Prepare Comparisons | Prepare comparisons |
| Select Variants | Select variants |
| SnpEff | SnpEff variant annotation |
| Split N Cigar Reads | Split N cigar reads |
| Variant Filtration | Filter variants |
| VCF Comparison | Compare VCF files |