The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
It is based on the <ahref="https://www.broadinstitute.org/gatk/guide/best-practices"target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
The pipeline accepts ```.fastq & .bam``` files as input.
The pipeline accepts ```.fastq & .bam``` files as <samplename>.
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## Tools for this pipeline
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@@ -22,6 +24,8 @@ The pipeline accepts ```.fastq & .bam``` files as input.
* Genotypegvcfs
* Variantannotator
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## Example
Note that one should first create the appropriate [configs](../config.md).
| run->RunID | ID | String | | Automatic filled by sample json layout |
| run->RunID | R1 | String | | |
| run->RunID | R2 | String | | |
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### sub Module options
This can be used in the root of the config or within the gatk, within mapping got prio over the root value. Mapping can also be nested in gatk. For options for mapping see: https://git.lumc.nl/biopet/biopet/wikis/Flexiprep-Pipeline
| Config Name | Name | Type | Default | Function |
The mapping pipeline has been created for NGS users who want to align there data with the most commonly used alignment programs.
The pipeline performs a quality control (QC) on the raw fastq files with our [Flexiprep](flexiprep.md) pipeline.
After the QC, the pipeline simply maps the reads with the chosen aligner. The resulting BAM files will be sorted on coordinates and indexed, for downstream analysis.
