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Title: Tools and workflow to produce VCF files from BAM files using Google Cloud Pipelines      
aggregation:
digital object
privacy:
not applicable
refinement:
uncurated
ID:
https://github.com/crimcc/bam2vcf
storedIn:
https://github.com/crimcc/bam2vcf
availability:
Available
creators:
Jong Cheol Jeong
keywords:
VCF; Sentieon; Google Genomics Pipeline; dsub; BAM; unmapped BAM, Google Cloud,GATK
dateReleased:
08-29-2018
description:
Although Google Cloud Genomics and Sentieon pipelines support robust tools to obtain high quality VCFs from BAM files, obtaining VCF files from these pipelines is not a trivial task. The problem is made worse when a BAM file has missing information in the header or an incomplete file structure to utilize GATK pipelines. The problem gets more complicated and challenging when the number of BAM files that needs to be processed is too large to rely on manual file management techniques and all of the files need to be transferred in and out of Google Cloud Storage. Therefore, we have implemented pipelines and source codes for producing VCF files from BAM files by utilizing Google Cloud Genomics and Sentieon pipelines.
types:
Source Code
authors:
Jong Cheol Jeong
description:
Although Google Cloud Genomics and Sentieon pipelines support robust tools to obtain high quality VCFs from BAM files, obtaining VCF files from these pipelines is not a trivial task. The problem is made worse when a BAM file has missing information in the header or an incomplete file structure to utilize GATK pipelines. The problem gets more complicated and challenging when the number of BAM files that needs to be processed is too large to rely on manual file management techniques and all of the files need to be transferred in and out of Google Cloud Storage. Therefore, we have implemented pipelines and source codes for producing VCF files from BAM files by utilizing Google Cloud Genomics and Sentieon pipelines.
ID:
https://github.com/crimcc/bam2vcf
acknowledges:
NIH Cloud Pilot
title:
Tools and workflow to produce VCF files from BAM files using Google Cloud Pipelines
dateReleased:
08-29-2018
description:
Although Google Cloud Genomics and Sentieon pipelines support robust tools to obtain high quality VCFs from BAM files, obtaining VCF files from these pipelines is not a trivial task. The problem is made worse when a BAM file has missing information in the header or an incomplete file structure to utilize GATK pipelines. The problem gets more complicated and challenging when the number of BAM files that needs to be processed is too large to rely on manual file management techniques and all of the files need to be transferred in and out of Google Cloud Storage. Therefore, we have implemented pipelines and source codes for producing VCF files from BAM files by utilizing Google Cloud Genomics and Sentieon pipelines.
name:
BAM files
description:
Although Google Cloud Genomics and Sentieon pipelines support robust tools to obtain high quality VCFs from BAM files, obtaining VCF files from these pipelines is not a trivial task. The problem is made worse when a BAM file has missing information in the header or an incomplete file structure to utilize GATK pipelines. The problem gets more complicated and challenging when the number of BAM files that needs to be processed is too large to rely on manual file management techniques and all of the files need to be transferred in and out of Google Cloud Storage. Therefore, we have implemented pipelines and source codes for producing VCF files from BAM files by utilizing Google Cloud Genomics and Sentieon pipelines.
name:
Tools and workflow to produce VCF files from BAM files using Google Cloud Pipelines
name:
Copyright 2018, UK Cancer Research Informatics
landingPage: https://github.com/crimcc/bam2vcf/blob/master/LICENSE
identifier:
CCREQ-2017-03-00028
funders:
NIH Cloud Pilot
count:
1
title:
Tools and workflow to produce VCF files from BAM files using Google Cloud Pipelines
storedIn:
https://github.com/crimcc/bam2vcf
description:
Although Google Cloud Genomics and Sentieon pipelines support robust tools to obtain high quality VCFs from BAM files, obtaining VCF files from these pipelines is not a trivial task. The problem is made worse when a BAM file has missing information in the header or an incomplete file structure to utilize GATK pipelines. The problem gets more complicated and challenging when the number of BAM files that needs to be processed is too large to rely on manual file management techniques and all of the files need to be transferred in and out of Google Cloud Storage. Therefore, we have implemented pipelines and source codes for producing VCF files from BAM files by utilizing Google Cloud Genomics and Sentieon pipelines.
size:
1.1MB
unit:
MB
ID:
SCR:016270
name:
CEDAR Workbench
abbreviation:
CEDAR
homePage: https://cedar.metadatacenter.org

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