cloud storage bucket error when handing vcf files of large size outside gcp(when uploading from pc).variant transforms and deep variant

[hze...@gmail.com]

I  am applying variant transforms on vcf files. i am facing issues when uploading vcf files size of 1 gb or 2gb outside the GCP, it returns error and secondly particullar  vcf files are viable to applied variant transforms or any  vcf file .

the other issue when running deepvariant . i am asking can deepvariant applied to only BAM and BAI files with regerence genome

thanks in advance

Haroon

[Paul Grosu]

Hi Haroon,

Have you tried one of the the following methods for transferring large files:

1) https://cloud.google.com/storage-transfer-service

2) https://cloud.google.com/storage-transfer/docs/create-manage-transfer-console

3) https://cloud.google.com/compute/docs/instances/transfer-files  

4) https://rclone.org/

To your second question, have you had a chance to review the quickstart guide at the following page: 

https://github.com/google/deepvariant/blob/master/docs/deepvariant-quick-start.md

Hope it helps,

Paul

[Saman Vaisipour]

i am facing issues when uploading vcf files size of 1 gb or 2gb outside the GCP, it returns error 

Could you please elaborate what is the problem? 

And for issues related to DeepVariant please submit an issue to their github repository. They are very quick in responding to the public issues.

Best,

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Saman Vaisipour |

Software Eng |

sam...@google.com |

519-513-5756