five-dollar-genome-analysis-pipeline

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five-dollar-genome-analysis-pipeline

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Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline

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# five-dollar-genome-analysis-pipeline
Workflows used for germline short variant discovery in WGS data

**This repository has been deprecated in favor of https://github.com/gatk-workflows/gatk4-genome-processing-pipeline**

### germline_single_sample_workflow :
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
- Picard 2.16.0-SNAPSHOT
- Samtools 1.3.1
- Python 2.7
- Cromwell version support 
  - Successfully tested on v37
  - Does not work on versions < v23 due to output syntax

### Important Note :
- The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables using the [GATK Tool and Tutorial Documentations](https://software.broadinstitute.org/gatk/documentation/).
- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://software.broadinstitute.org/gatk/download/bundle).
- 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://software.broadinstitute.org/gatk/documentation/article?id=12521).
- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team/) , [FireCloud](https://gatkforums.broadinstitute.org/firecloud/categories/ask-the-firecloud-team) or [Terra](https://broadinstitute.zendesk.com/hc/en-us/community/topics/360000500432-General-Discussion) , [WDL/Cromwell](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).
- Please visit the [User Guide](https://software.broadinstitute.org/gatk/documentation/) site for further documentation on our workflows and tools.

### LICENSING :
Copyright Broad Institute, 2019 | 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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