invalid VCF file

leulmi selma

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May 7, 2024, 1:41:22 PMMay 7

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Hi,

I am trying to upload a phased.vcf along with a phased.gtf but I am having this error message : invalid VCF file: missing fileformat line (object File).

However, I have inspected the vcf file and I found that the ##fileformat=VCFv4.2 is there ... Any advice/idea on how to solve this ?

All the best,

Selma.

igv-help

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May 7, 2024, 2:49:47 PMMay 7

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Hi Selma,

It's not something we've come across before. If you can share an excerpt from your file that shows the same behavior we can take a look? We don't need the whole file, a small file that still displays the same behavior would be good. For example, make a copy and delete most of the data, and after you've verified it still has the problem you can send it to us privately at igv-...@broadinstitute.org.

Helga

igv-help

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May 7, 2024, 2:51:58 PMMay 7

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Actually, before you send us anything. You don't mention which version of IGV you are running. If you are not running the latest (2.17.4), can you first try your file with the latest IGV and see if that makes a difference.

leulmi selma

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May 7, 2024, 3:45:52 PMMay 7

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Many thanks for your reply. I used the IGV Web App in a web browser. Can this be the reason ?

igv-help

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May 7, 2024, 4:06:58 PMMay 7

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I have not been able to reproduce your problem in IGV-Web. It might not be the file but rather how it's accessed from the app. Where is the file? How are you loading it into the app? Does it work if the file is on your local file system and you load it from there?

leulmi selma

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May 7, 2024, 10:10:47 PMMay 7

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I am using a remote desktop on a HPC cluster, and my files are stored in the same cluster. I have loaded bam files before and it all worked well. So I'm not sure what is the issue with this VCF file.

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