Fork Purpose:
Added index input to several tasks that require them, but for some reason did not have any, which lead to workflow failing. Changed import of tasks to local instead of https://... See commit: 0e689abeea58fe03768bd82cbdb15e7113f5f374
gatk4-exome-analysis-pipeline
Purpose :
This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
Requirements/expectations :
- Human exome 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:
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- filenames all have the same suffix (we use ".unmapped.bam")
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- files must pass validation by ValidateSamFile
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- reads are provided in query-sorted order
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- all reads must have an RG tag
- GVCF output names must end in ".g.vcf.gz"
- Reference genome must be Hg38 with ALT contigs
- Unique exome calling, target, and bait .interval_list obtained from sequencing provider. Generally the calling, target, and bait files will not be the same.
Output :
- Cram, cram index, and cram md5
- GVCF and its gvcf index
- BQSR Report
- Several Summary Metrics
Software version notes :
- GATK 4 or later
- Cromwell version support
- Successfully tested on v44
- Does not work on versions < v23 due to output syntax
Important Notes :
- 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.
- Please visit the User Guide site for further documentation on our workflows and tools.
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 or Terra.
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.