gatk4-genome-processing-pipeline

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gatk4-genome-processing-pipeline

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Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

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# gatk4-genome-processing-pipeline

#### *- This repo has been archived, the workflows new repository location is [broadinstitute/warp](https://github.com/broadinstitute/warp/tree/develop/pipelines/broad/dna_seq/germline/single_sample/wgs)*

Workflows used for germline processing in whole genome sequence data.

### WholeGenomeGermlineSingleSample :
This WDL pipeline implements data pre-processing and initial variant calling (GVCF
generation) according to the GATK Best Practices (June 2016) for germline SNP and
Indel discovery in human whole-genome sequencing data.

#### Requirements/expectations
- Human whole-genome paired-end sequencing data in unmapped BAM (uBAM) format
- One or more read groups, one per uBAM file, all belonging to a single sample (SM)
- Input uBAM files must additionally comply with the following requirements:
- - filenames all have the same suffix (we use ".unmapped.bam")
- - files must pass validation by ValidateSamFile
- - reads are provided in query-sorted order
- - all reads must have an RG tag
- Reference genome must be Hg38 with ALT contigs

#### Outputs 
- Cram, cram index, and cram md5 
- GVCF and its gvcf index 
- BQSR Report
- Several Summary Metrics

### Software version requirements :
- GATK 4.0.10.1 and GATK 3.5
 - By default, HaplotypeCaller will perform variant calling using GATK 3.5, which is what is used in Broad Production. To use GATK4, specify `use_gatk3_haplotype_caller=false` in the inputs.json. 
- Picard 2.20.0-SNAPSHOT
- Samtools 1.3.1
- Python 2.7
- Cromwell version support 
  - Successfully tested on v53

### Important Notes :
- The provided JSON is a generic ready to use example template for the workflow. It is the user’s responsibility to correctly set the reference and resource variables for their own particular test case using the [GATK Tool and Tutorial Documentations](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591).
- Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
- For help running workflows on the Google Cloud Platform or locally please
view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).
- Please visit the [User Guide](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591) site for further documentation on our workflows and tools.
- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360035890811).

### Contact Us :
- The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : [GATK](https://gatk.broadinstitute.org/hc/en-us/community/topics) or [Terra](https://support.terra.bio/hc/en-us/community/topics/360000500432).

### LICENSING :
Copyright Broad Institute, 2020 | BSD-3
This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.
- [GATK](https://software.broadinstitute.org/gatk/download/licensing.php)
- [BWA](http://bio-bwa.sourceforge.net/bwa.shtml#13)
- [Picard](https://broadinstitute.github.io/picard/)
- [Samtools](http://www.htslib.org/terms/)

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