Hello, I am looking for ways to process the vcf files. I tried processing using the swish alpha knife and took a long time to upload the data to the cloud. I also observed for each chromosome, we have multiple sets of vcfs.
1.) I want to know how these were combined together to process.
2.) Are there any ways to process these files or do I need to submit multiple bash jobs to process each vcf at a time?
Please do let me know how to proceed further.
Swiss Army Knife (SAK) is IMO a great tool for processing both, i.e. one vcf at time or multiple files in one job. If I am not wrong, Swiss army knife can take an array as input, so you should be able to specify multiple files. Moreover, SAK can read data via dxfuse, that means you can directly read data from /mnt/project/Bulk/...
JupyterLab is great for interactive sessions and also has mounted dirs, so you can read data via /mnt/project/Bulk/...
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1) I think you will need to decide which files you want to work with (WES / WGS, VCF / pVCF).
This protocol applies to all UK Biobank whole exome sequencing data sets, including 200k, 300k, 450k, and the final release OQFE data sets:
https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/protocol-for-processing-ukb-whole-exome-sequencing-data-sets
2) For processing, this would depend on your use case and the type of analysis you want to do. As a first step, you may review the following doc page:
https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/working-with-bulk-data-files
Swiss Army Knife (SAK) is IMO a great tool for processing both, i.e. one vcf at time or multiple files in one job. If I am not wrong, Swiss army knife can take an array as input, so you should be able to specify multiple files. Moreover, SAK can read data via dxfuse, that means you can directly read data from /mnt/project/Bulk/...
JupyterLab is great for interactive sessions and also has mounted dirs, so you can read data via /mnt/project/Bulk/...
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