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Converting RDML files (real time pcr markup language) into .vcf

Hi everyone, I'm very new to bioinformatics so please bear with me,

I have some simple genotyping results for a group of samples and a couple of SNPs I got from my PCR machine (Applied Biosystems® ViiA™ 7 Real-Time PCR System).

I need to convert these results to a .vcf file. I've looked up what .vcf is and what it needs (https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format) but I still don't understand how I can make this file properly. I'm sure I'm missing something here.

I saw that the QuantStudio Real-Time PCR software that I use for the machine can export results as xlsx, txt or rdml (Real-time PCR Data Markup Language). Can any of these formats be converted into a .vcf file?

I've searched here as well and saw that there is a way to convert PED files to .vcf but it requires a .map and I have no clue how to generate one for my data; I'm only familiar with .ped files and .info files while trying to run Haploview.

Thanks!

vcf
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written by Nafeesa • Nafeesa

I have some simple genotyping results for a group of samples and a couple of SNPs I got from my PCR machine (Applied Biosystems® ViiA™ 7 Real-Time PCR System).

what does it look like ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre, thanks for replying. I would like to attach an example of the results file I get from the program here, but I don't know how. I've attached a screenshot from the program instead. exampleenter image description here

I export just the sample names and the allele call as an excel sheet for my results and analysis, but there's obviously a lot more information. Still, I don't know how I can convert this into .vcf, or if I'm missing anything.

I need to do this because I was asked to upload the genotyping results to a data repository (https://www.ebi.ac.uk/eva/?Submit-Data).

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written by Nafeesa • Nafeesa

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