How can I create an Illumina report in Linux using IDAT files?

Question

[Ginevra]

Hello everyone!

I am looking for a way to create an Illumina report, starting from IDAT files. I know how to do it with GenomeStudio in Windows, but I would need to produce the same file (with BAF and LRR columns) in the Linux environment. Do you know how I can do it? Thanks in advance for your reply!

Ginevra

[Kevin Blighe]

I presume that you mean that you want to use GenomeStudio on linux? - have you seen this previous answer - A: Automate Illumina GenomeStudio With Python Script ?

[Ginevra]

Thanks for the suggestion, I read the answer given on the topic. My point is that I just need the BAF and LRR information and not the gtc. Does the AutoConvert do that? Unfortunately, I am not very good at coding.

Answer 1

[Kevin Blighe]

Are you implying that you have absolutely no access to GenomeStudio on Windows? - that would obviously be the easiest solution. If this is the case, then ignore my previous post.

There seems to various ways to calculate LRR and BAF from IDAT, but nothing that seems as simple as point-and-click.

For example, THIS BCFtools plugin can do it, but it outputs the LRR and BAF encoded in VCF tags (which you could, technically, extract thereafter). The R package crlmm can also do it, but requires coding.

[Giulio Genovese]

After you have converted your IDATs to GTCs using Illumina's iaap-cli command, the following command will produce a GenomeStudio-like table:

bcftools +gtc2vcf -t GT,BAF,LRR -b <file.bpm> -f <file.fasta> -Ot <A.gtc> <B.gtc> ...

It can be further customized to yield the columns you need

Answer 2

[curious]

I just went though this ordeal on my end. You could convert IDAT to GTC using either autoconvert, which can run on linux with the wine compatibility layer if you google. Also illumina is developing a linux CLI to convert IDAT to GTC: https://support.illumina.com/downloads/iaap-genotyping-cli.html

I used this CLI, it works pretty well.

Once you have the GTC files you might want to to look at the GTC specification:

https://github.com/Illumina/BeadArrayFiles/blob/develop/docs/GTC_File_Format_v5.pdf

It requires coding to extract LRR and BAF from GTC but its in there.

illumina has a repo of some python classes that can help generate Final Reports from GTC from the command line and could be run in a linux environment. That is where I would start playing if you don't know coding too well but need to ease in:

https://github.com/Illumina/BeadArrayFiles

I used these too, not really well documented but well coded. Albeit in python 2 which might add a barrier in 2020

Maybe someone else knows a better way though

[Ginevra]

How can I see the content of the .gtc file in order to extract the information that I need? I would need to open this file but I don't know how.

[curious]

Unless there is a way I don't know about you need to open it with a programming language like python and parse according to the specification I linked. Or use the pre-build illumina parser which still requires programming with python

[Giulio Genovese]

You can look at the full content of a GTC file with the following command:

bcftools +gtc2vcf -v <file.gtc>