Problem loading .genotypes.vcf.gz file

[Naveen Mathew Nathan S.]

Hi,

I'm new to IGV. I have limited background in biology.

I'm trying to load a .genotypes.vcf.gz that has data on chr1. Steps followed:

1) File > Load from File

2) Selected the .genotypes.vcf.gz file. Verified that there is an associated index file with the same name .genotypes.vcf.gz.tbi

3) Clicked Open

This loads a track. However, I faced the following issues:

1) no update to the chromosome ideogram

2) nothing displayed in track. Display mode was set to 'Expanded'

I've attached a screenshot for reference. Please help me solve these issues.

[James Robinson]

You need to zoom in to see features,  did you see the text on the track?  There are too many features to show at whole chromosome level.    I'm not sure what you expected to see on the ideogram.

Jim

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[Naveen Mathew Nathan S.]

Hi Jim,

I clicked 'Set Feature Visibility Window' and entered 0. Still I was not able to view anything on the track.

I was unable to find the option to zoom in.

I also found a message 'No Variants Found' in the track. PFA.

Regards,

Naveen

On Thursday, April 27, 2017 at 7:18:53 AM UTC+5:30, Jim Robinson wrote:

You need to zoom in to see features,  did you see the text on the track?  There are too many features to show at whole chromosome level.    I'm not sure what you expected to see on the ideogram.

Jim

On Wed, Apr 26, 2017 at 6:28 PM, Naveen Mathew Nathan S. <pg13s_...@mandevian.com> wrote:

Hi,

I'm new to IGV. I have limited background in biology.

I'm trying to load a .genotypes.vcf.gz that has data on chr1. Steps followed:

1) File > Load from File

2) Selected the .genotypes.vcf.gz file. Verified that there is an associated index file with the same name .genotypes.vcf.gz.tbi

3) Clicked Open

This loads a track. However, I faced the following issues:

1) no update to the chromosome ideogram

2) nothing displayed in track. Display mode was set to 'Expanded'

I've attached a screenshot for reference. Please help me solve these issues.

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[James Robinson]

That means there are no records for that chromosome in the file.  

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