Generating Depth of Coverage files from vcf.

Question

[Francisco]

Does anyone know if it's possible to obtain a depth of caverage file from a vcf format file? I'm looking to create new files with depth of coverage information in the following formats: VDR, EGFR, RYR1 or GDF.

I ned this depth of coverage information file to run Stargazer software. Also I have to use previously generated vcf files, so no chance of using BAM files to call variants again and in the process obtain the depth of coverage file.

Thanks a lot for your time and help.

[Pierre Lindenbaum]

in the following formats: VDR, EGFR, RYR1 or GDF.

looks like gene names to me, not "format"

[liorglic]

I'm not familiar with the formats you mention, but AFAIK, VCF files cannot be used to obtain depth data, since they do not contain that type of information. Depth of coverage is usually derived from BAM files, or other formats describing read mappings.
Can you provide a snippet from your VCF file and an example of the desired output?

Answer 1

[Divon]

If you're lucky, variants might include the DP field in either the INFO field or each sample, or both.

Answer 2

[sbstevenlee]

Wow, I'm very late to the party here! As the developer of Stargazer, I'd like to provide some insights:

1. VDR, EGFR, and RYR1 are indeed gene names. These genes serve as a control when normalizing read depth in the target gene (e.g. CYP2D6) to compute per-base copy number.

2. In contrast, GDF is a file format. If you look at the original paper: "For convenience, we will refer to this output as a target GDF (GATK-DepthOfCoverage format) file".

3. If you don't have access to BAM files, then it's not possible to perform structural variation detection.

4. However, it doesn't necessarily mean that you can't perform PGx genotyping at all. I've developed a new PGx genotyping tool called PyPGx. You can use PyPGx to perform PGx genotyping with VCF only. For more details, please see the docs.