Closed JCBNim closed 9 months ago
Can you please describe what you're either asking or requesting?
Hello, I want to know if the "AD" format requires an integer or if a number with decimals is possible. The Pharmcat software tells me the following message with the numbers detailed in the screenshot: "VCF Unexpected AD format number: '2'. Treating number as '.' and ignoring AD field.
The attached file is a screenshot of part of my VCF generated by "Sophiagenetics DDM" where you can see the AD format
I want to know if the "AD" format requires an integer or if a number with decimals is possible.
I'm going to answer your question with another question: do you understand what the AD field represents? If not, refer to the "AD and DP" section here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format
TL;DR - Since it represents the # of reads, it must be an integer.
The Pharmcat software tells me the following message with the numbers detailed in the screenshot: "VCF Unexpected AD format number: '2'. Treating number as '.' and ignoring AD field.
This error is not talking about the VALUE you have, it refers to the INFO header for the AD field.
I will improve the error message to: INFO header for AD has unexpected number (2). Expecting 'R'. Treating number as '.' and ignoring AD field.
See section 1.2.2 in the VCF spec for details.
TL;DR - You should have an AD value for each possible allele, which is represented by "R".
Do you want to request a feature or report a bug? a bug
What is the current behavior? VCF Unexpected AD format number: '2'. Treating number as '.' and ignoring AD field.
If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar.
What is the expected behavior?
What is the motivation / use case for changing the behavior?
Please tell us about your environment:
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, e.g. stackoverflow, gitter, etc.)
Good morning, the issue about the AD format linked to the VCF I use. The HTML report doesn't run for some genes perhaps due to the AD format used in the VCF given by SophiaGenetics. Could you please help us. Thanks. JC BOYER