Google Cloud - VCF Creation Support from .bam
0
0
Entering edit mode
4.4 years ago

What is the best way to use Google Cloud/Genomics to create VCF files from .bam files? Is there specialized support or a package, or should I create a VM and install tools like GATK to do this?

Bam vcf google cloud google genomic • 1.4k views
ADD COMMENT
0
Entering edit mode

Take a look at this online documentation for ideas. Google genomics cookbook documentation.

ADD REPLY
0
Entering edit mode

Use Genomics Pipeline API or other workflow languages (CWL or WDL/Cromwell) supported by Genomics API to construct a pipeline, and then build/push docker images for each tool you need to container registry. Finally, launch the pipeline. Another way is to use Google Dataflow, but I'm not familiar with this method :(

You can read the documents and source codes of this example from Google Genomics Cookbook: https://github.com/googlegenomics/pipelines-api-examples/tree/master/cwl_runner

ADD REPLY

Login before adding your answer.

Traffic: 1887 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6