"No Variants Found" in any .vcf file

[Rebecca Cole]

Hi all,

I have recently inherited a number of vcf files from a former member of our group, which I would like to view in IGV. I have already installed the appropriate reference genome (the same that was used to call variants) and seem to be able to load the .vcf files without difficulty, however IGV does not display a single variant in any part of the genome, nor in any sample Instead I just get the message "No Variants Found". This is despite the fact that, when I open the vcf file, I can see many variants listed. In short; I expected that when I loaded a vcf file, I would see variants marked against the reference genome, but instead I simply receive the message "No Variants Found."

I am using IGV 2.3 for Windows.

A screenshot of what I'm seeing is attached.

Please let me know if there is any other information I can provide that would be helpful; I'm very new to all of this so am not sure precisely what information I should give.

Thanks in advance,

Rebecca

[James Robinson]

Hi,  I assume you have jumped to an exact location that a variant exists in the VCF file  (columns 1 and 2)?   

I'll probably need a sample of the VCF to investigate this, and perhaps the fasta but lets start with the vcf.   I will send you a dropbox link.

Jim

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[Rebecca Cole]

Hi Jim,

I have uploaded some examples of the affected files (I hope to the right place); they all behave in the same way. I had not actually zoomed in on any particular bit of sequence, but I can scan across the entire genome at that and any other resolution and the same message of no variants found always displays, despite their being variants recorded in the vcf files.

I hope this helps, let me know if there's anything else I can do.

Cheers,

Rebecca

On Tuesday, 4 October 2016 16:16:32 UTC+1, Jim Robinson wrote:

Hi,  I assume you have jumped to an exact location that a variant exists in the VCF file  (columns 1 and 2)?   

I'll probably need a sample of the VCF to investigate this, and perhaps the fasta but lets start with the vcf.   I will send you a dropbox link.

Jim

On Tue, Oct 4, 2016 at 3:02 AM, Rebecca Cole <rc1...@bristol.ac.uk> wrote:

Hi all,

I have recently inherited a number of vcf files from a former member of our group, which I would like to view in IGV. I have already installed the appropriate reference genome (the same that was used to call variants) and seem to be able to load the .vcf files without difficulty, however IGV does not display a single variant in any part of the genome, nor in any sample Instead I just get the message "No Variants Found". This is despite the fact that, when I open the vcf file, I can see many variants listed. In short; I expected that when I loaded a vcf file, I would see variants marked against the reference genome, but instead I simply receive the message "No Variants Found."

I am using IGV 2.3 for Windows.

A screenshot of what I'm seeing is attached.

Please let me know if there is any other information I can provide that would be helpful; I'm very new to all of this so am not sure precisely what information I should give.

Thanks in advance,

Rebecca

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[James Robinson]

Hi, got the vcf files.  I can't load them directly without the fasta, sorry I should have asked.   Anyway,  could you try loading the file  Srat_53a_334826_ED53_lanes.vcf and jumping to this position (just cut and paste into the "Go" box and hit "Go")

  Sratt_Chr2_000001:154

Then make a screenshot of what you see.  Thanks.

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[James Robinson]

I was able to load it by renaming the chromosome to "chr2", then using human as a reference.  Here's what I see for that position

​

[Rebecca Cole]

Hi,

This data is not from human but from a nematode, Strongyloides ratti. I've uploaded the .fa I am using as the reference genome into the same location as the .vcf files, which I hope will help. I did notice though that there is a mismatch between what the chromosomes are called in the .fa and what they're called in the .vcf; perhaps this is the problem? Is there a simple way to change a chromosome name? I tried jumping to that location as requested anyway but I received an error message:

 

Thanks again for all your help,

Rebecca

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[James Robinson]

I understand that.   The problem here is there is no sequences in your fasta that match the names in your vcf (e.g. Sratt_Chr2_000001).    I should have asked you to check that up front, but I thought you said this was the fasta used to generate the VCFs.    

Here are the sequence names from the fasta file

chr1

chrX_scaffold1

chrX_scaffold2

SRAE_chrX_scaffold3

SRAE_scaffold1

SRAE_chrX_scaffold4

SRAE_chrX_scaffold5

SRAE_chrX_scaffold6

SRAE_scaffold2

SRAE_scaffold3

SRAE_chrX_scaffold7

SRAE_chrX_scaffold8

SRAE_scaffold4

SRAE_scaffold5

SRAE_scaffold6

SRAE_chrX_scaffold9

SRAE_chrX_scaffold10

SRAE_scaffold7

SRAE_scaffold8

SRAE_scaffold9

SRAE_scaffold10

SRAE_scaffold11

SRAE_scaffold12

SRAE_scaffold13

SRAE_scaffold14

SRAE_scaffold15

SRAE_scaffold16

SRAE_scaffold17

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SRAE_scaffold20

SRAE_scaffold21

SRAE_scaffold22

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SRAE_scaffold123