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Error Code 1 for VCF import

asked 2024-05-23 12:24:08 -0600

John H gravatar image

Hi, can anyone help me with this error 1 code I receive when I import my VCF data into Genome Browse? I've tried both the long-hand folder search and the quicker drag and drop. It shows it in the Plot View but says: "Failed to open for writing: C:/Users.........snp-indel.genome/vcf.gz (error code 1)"

Prior to importing. I unzipped this compressed file using winzip and put it in a separate folder, so not sure why it's showing the .gz suffix on the end of the file name. It's just a .vcf file i asked GB to import.

I checked the Win11 folder properties and full read/write access is allowed (saw an earlier BAM import post on the community that suggested this)

Any help would be appreciated as the GB software looks very useful! If it helps, I'm using version 3.1.0 and I've downloaded the full reference genome for GRCh38 too Thanks, John

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answered 2024-05-29 22:51:20 -0600

Hi John,

GenomeBrowse can only read VCF files directly that have a specific genomic compression and indexing perform (bgzip) .

If it detects a raw VCF file, it will attempt to write a side-by-side .vcf.gz and .vcf.gz.tbi file on the fly. GenomeBrowse does require write permissions for this step, and for some reason that is not working with your file.

Another solution, is you can run the VCF through the Convert process in the Tools > Manage Data Sources dialog. This converts it to the native annotation track form TSF and puts the file in the annotation user directory, which can then be plotted.

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Asked: 2024-05-23 12:24:08 -0600

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Last updated: May 29