# Sentieon Germline Whole Genome Sequencing Analysis

Align reads to the reference genome, call variants, and calculate quality metrics using Sentieon.

## Align reads to the reference genome, call variants, and calculate quality metrics using Sentieon.

This workflow implements the [Sentieon® Genomics](https://www.sentieon.com/) software, a set of software tools that perform highly accurate and computationally efficient analysis of genomic data. This workflow performs read alignment, duplicate marking, base quality score recalibration (BQSR), and variant calling steps. The workflow is designed for use with a variety of reference genomes, which are downloaded as part of workflow execution. The workflow also computes quality metrics on the deduplicated alignments and produces various plots which can be used to quickly inspect sample quality.

The workflow can optionally output a gVCF rather than a VCF file, which can be combined with other sample gVCFs for use in joint genotyping.

This workflow was developed by the Sentieon development and is written in [Workflow Description Language (WDL)](https://openwdl.org/). Further documentation can be found [here](https://support.sentieon.com/manual/introduction/intro/).

## Workflow Inputs

The workflow can be run using either paired FASTQ or aligned BAM/CRAM files. If using the FASTQ entrypoint, `r1_fastq`, `r2_fastq`, and `read_groups` must be defined. If using the BAM/CRAM entrypoint, `input_aln` and `input_aln_idx` must be defined.

| Input                  | Description                                                                                             |
|-----------------------|---------------------------------------------------------------------------------------------------------|
| `r1_fastq`           | R1 fastq files                                                                                        |
| `r2_fastq`           | R2 fastq files                                                                                        |
| `read_groups`        | Sample read groups                                                                                     |
| `input_aln`         | Input alignment (BAM/CRAM) files                                                                      |
| `input_aln_idx`     | Input alignment (BAM/CRAM) index files                                                                |
| `reference_name`     | The name of the human reference genome build. (‘hg38_alt’, ‘hg38_gatk’, ‘hg38’, ‘hg38_noalt’, ‘hs38’, ‘b37_gatk’, ‘b37’, ‘hs37d5’, ‘hg19’, ‘ucsc_hg19’) |
| `run_dedup_and_qc`   | If `true`, mark duplicates and output QC metrics and plots. 
| `output_gvcf`        | Output variant calls in the gVCF format instead of VCF 
| `dnascope_model`     | The Sentieon DNAscope variant calling model                                                             |
| `canonical_user_id`  | Your account’s AWS canonical user ID. Used to acquire a Sentieon license                             |
| `sentieon_docker`    | Sentieon docker image                                                                                  |
| `is_pcr_free`        | Set to `true` if the data is processed with a PCR-free library prep                                     |
| `n_threads`          | Number of vCPUs to allocate for the task                                                                |
| `memory`             | Memory to allocate for the task                                                                          |

## Workflow Outputs

The workflow produces variant calls in either VCF or gVCF format will be produced. Other outputs will depend on the options selected.

| Output                  | Description                                                                                             |
|------------------------|---------------------------------------------------------------------------------------------------------|
| `calls_vcf`            | Variant calls in VCF or gVCF format                                                                    |
| `calls_vcf_tbi`       | Variant calls index                                                                                     |
| Metrics and reads files | Metrics and reads files are produced if `run_dedup_and_qc` is set to `true`.                           |

|     |     |
|----------------------|--------------------------------------------------------------------------------------------------------|
| aligned_reads        | Aligned and duplicate marked reads                                                                      |
| aligned_index        | Index for `aligned_reads`                                                                              |
| dedup_metrics        | File containing the metrics data from the deduping stage                                               |
| mq_metrics           | File containing metrics quantifying the mean base quality score for each sequencing cycle              |
| qd_metrics           | File containing metrics quantifying the number of bases with a specific base quality score             |
| gc_summary           | Summary of the GC bias in the reference and the sample                                                |
| gc_metrics           | File containing metrics quantifying the GC bias in the reference and the sample                       |
| as_metrics           | File containing statistics about the read alignment                                                     |
| is_metrics           | File containing metrics quantifying the statistical distribution of insert sizes                        |
| mq_plot              | Plot of the `mq_metrics`                                                                               |
| qd_plot              | Plot of the `gd_metrics`                                                                                |
| gc_plot              | Plot of the `gc_metrics`                                                                                |
| is_plot              | Plot of the `is_metrics`                                                                                |
| `bqsr_table`          | Sample recal table output by running BQSR. Base quality score recalibration will run if no custom `dnascope_model` is provided. |

## Containers

The latest version of the Sentieon Docker image can be run by following the instructions listed [here](https://github.com/Sentieon/sentieon-docker).