IGV tools cannot determine file format

[Matthew Romero]

Hello, I have been trying to use IGV desktop app on Windows in order to view .vcf files output from NanoVar and NanoSV. 

I see that I must preprocess the data by indexing with IGV tools, and that formats VCF4.0 and up are acceptable, which NanoVar output is however when I upload my .vcf files I get the following error. 

java.lang.RuntimeException: Cannot determine file format: C:\Users\lab\Desktop\test_hg38.nanovar.total.vcf
    at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:93)
    at org.igv/org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:53)
    at org.igv/org.broad.igv.tools.CoverageCounter.parse(CoverageCounter.java:300)
    at org.igv/org.broad.igv.tools.IgvTools.doCount(IgvTools.java:869)
    at org.igv/org.broad.igv.tools.IgvToolsGui$5.doInBackground(IgvToolsGui.java:455)
    at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)
100.0%
Done

The only thing I did before uploading my file to igv-tools was copy over from the mounted drive of wsl to my desktop, I was not sure what to save the file type so I made it a .txt file then changed extension to .vcf

If there are any blatant errors that can help fix this please let me know.

Here is my file I have been testing with.

[igv-help]

Hi,

From the error messages, it looks like you tried to run the "Count" command, rather than the "Index" command.
When you open up the igvtools window, please make sure to select "Index" from the dropdown list for the Command field.

Helga

[Matthew Romero]

Hi Helga,

Oh that is my bad, when I run index it works and I get the right file. However, when I load the .idx file into IGV I don't see any data even though the indexing completed without any problems.

[igv-help]

You do not load the index file, you load the vcf file.  The index file is found automatically.  

[Matthew Romero]

Oh my mistake. I tried uploading my test .vcf files after indexing and I see that I still do not see any data. 

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Matthew Romero

Research Technician, Tecan @ Cue Health Inc.

m.ro...@cue.me

[James Robinson]

As the message indicates, you need to zoom in.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAN1e4z%2B2vzXaSwNK6afb46zuUQF_sYR3LdMvvS4v9r2jdesnGQ%40mail.gmail.com.

[Matthew Romero]

My mistake again, I can see it now. Thank you for your help and patience with this.