Issues working with VCF2db

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Mary Makarious

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Aug 22, 2018, 6:24:25 PM8/22/18
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Hello,
My following workflow looks like the following

(Fast-forward a bit...)

  1. VT to decompose (no issues here)
  2. VT to normalize (issues here so...)
  3. BCFTools to normalize (no issues here)
  4. Ensembl VEP to annotate the .vcf (no issues here)

This is where I have the problem.
I get the following errors when I try to load the annotated file into VCF2db to have it work with GEMINI after 

Pasted below is the error message:
Traceback (most recent call last):
File "/usr/local/apps/vcf2db/2017.12.11/vcf2db.py", line 916, in <module>
impacts_extras=a.impacts_field, aok=a.a_ok)
File "/usr/local/apps/vcf2db/2017.12.11/vcf2db.py", line 222, in __init__
self.vcf = cyvcf2.VCF(vcf_path)
File "cyvcf2/cyvcf2.pyx", line 187, in cyvcf2.cyvcf2.VCF.__init__

IOError: my.vcf if not valid bcf or vcf


Obviously, however, it is a valid vcf.

What am I doing wrong?

Many thanks,
MM.

Mary Makarious

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Aug 22, 2018, 6:25:52 PM8/22/18
to gemini-variation
Important to note I am working with the hg38 assembly and WGS, hence why I couldn't try to directly load into gemini.

Best,
MM.

Brent Pedersen

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Aug 23, 2018, 10:23:25 AM8/23/18
to mb.mak...@gmail.com, gemini-variation
Hi Mary,
can you show the output of `bcftools view $vcf > /dev/null` ? where
$vcf is the one you're having trouble loading?

-Brent

Mary Makarious

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Aug 23, 2018, 11:26:42 AM8/23/18
to gemini-variation

Mary Makarious

11:25 AM (0 minutes ago)
to bpederse
So when I try to do that, I am also getting an error reporting that it is not a valid file type.
I wonder why, however, since all I did was use Ensembl's VEP to annotate?

Perhaps, would you be willing to share the commands you use with VEP to annotate using an hg38 ref. file that results in a "valid" .vcf?

I tried to run the bcftools view command on the .vcf I used prior to annotating, it seems to have no trouble reading it.

Best,
MM.

On Wednesday, August 22, 2018 at 6:24:25 PM UTC-4, Mary Makarious wrote:

Brent Pedersen

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Aug 23, 2018, 12:33:37 PM8/23/18
to Mary Makarious, gemini-variation
Hi Mary, you can see an example VEP command in the gemini documentation.
Perhaps you didn't tell VEP that you wanted VCF output. You could look at the first few lines to see if it looks like VCF.
-Brent
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