VCF format

[erick-dorlass]

Hi,

I am intending to use cmvdrg software for detecting possible resistance variants in a CMV VCF file. However, it seems like my VCF file input is not valid for cmvdrg. This is the error message i get:

arguments imply differing number of rows: 44, 0, 1
Calls: call_resistance -> read_input -> data.frame

My VCF file (v4.2) is a Freebayes output. If I'm using a VCF file as an input, it must be generated with Varscan?

[ojcharles]

Hey, so glad you're interested in using this tool! So this repository is not really supported as there is a (unpublished) herpes-wide version now, you can access it here http://cmv-resistance.ucl.ac.uk/herpesdrg.
If that webserver errors when you use VCF (v4.2) file, please email me an example of your file to [email protected] and i'll make the changes required.
Thanks, Oscar

[erick-dorlass]

Thank you for responding so fast.

Actually, our goal is to use the cmvdrg tool as component in a pipeline, I don't think that a web based tool would work.
If you think that you could still help me, I could send you an e-mail with the vcf file

[ojcharles]

Hi Erick, Absolutely. Send me an example file and I'll update this (and my herpes generic tool). Oscar

…

On Wed, 26 Oct 2022 at 20:19, erick-dorlass ***@***.***> wrote: Thank you for responding so fast. Actually, our goal is to use the cmvdrg tool as component in a pipeline, I don't think that a web based tool would work. If you think that you could still help me, I could send you an e-mail with the vcf file — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AG3JEBEQQERYRQ6L42YB5DTWFF73RANCNFSM6AAAAAARO5ETVQ> . You are receiving this because you commented.Message ID: ***@***.***>

[lexleong]

@ojcharles
We are also hoping to use this tool for our cmv wgs work for detection of mutations. We had the same issues where it has been giving us the error for fasta/vcf files that we tried.

Error in read_input(infile, global = global) : 
  Check your variant call file is in .tab, .vcf format 
 or check your fasta file has the .fa, .fas or .fasta extension

[ojcharles]

Hi lexleong!
Can you clarify if this is the cmvdrg package, or the webserver? The webserver should have the changes that solved Ericks issue above.
I want to point out this repo isn't being developed on as I'm just finalising a herpes-wide db and tool.
If the webserver does not work, you can email [email protected] with an example error causing file and I will debug.
regards

[lexleong]

Hi Charles,
I have tried both cmvdrg package, and the webserver.
I will email you directly.
Cheers,
Lex

[raquelriyuzo]

Hi, I also had the same error reported when I tested the tool with the Git example (A10.vcf).
Error in read_input(infile, global = global) :
Check your variant call file is in .tab, .vcf format
or check your fasta file has the .fa, .fas or .fasta extension

I tried to access this page: http://cmv-resistance.ucl.ac.uk/herpesdrg, but it doesn't exist. Is there another way to resolve this error?

Thank you very much!

[ojcharles]

Hi there,
This repo is no longer maintained. Please see https://github.com/ojcharles/herpesdrg

Also I'm sorry that you could not get the webserver to work, It appears to be running for me.
http://cmv-resistance.ucl.ac.uk/herpesdrg/ if you continue to have problems please email me at [email protected]

Regards,
Oscar