AD Format

[JCBNim]

• 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:

  • PharmCAT Version: ???
  • JDK Version: [ JDK8 | OpenJDK | etc ]
  • Environment: [ Windows | macOS | Linux distro | etc ] macOS

• 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

[whaleyr]

Can you please describe what you're either asking or requesting?

[JCBNim]

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

[markwoon]

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".