Now supports extracting gencall scores (GCALL) as real numbers #74
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This is essentially what it used to do. I'm thinking it may be better to just change GS back to what you have here with GCALL as the phred-scaled score may be useful for parsing via bcftools, but is not actually a good metric for GS. For the gentrain score, that is encoded in the cluster file (egt) and out of the scope of this tool. This tool may help you out: |
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Thanks for pointing me to the locus_summary script. I'll definitely check it out.
And yes, at least for us we really wanted access to the raw value-the current GQ tag is likely fine for most folks (though some purists might object as it's not quite the same thing as the genotype quality).
Regardless, I appreciate your help and for maintaining this tool, and for responding so quickly!
-August
From: jzieve ***@***.***>
Sent: Thursday, April 27, 2023 1:32 PM
To: Illumina/GTCtoVCF ***@***.***>
Cc: Woerner, August ***@***.***>; Author ***@***.***>
Subject: [EXT] Re: [Illumina/GTCtoVCF] Now supports extracting gencall scores (GCALL) as real numbers (PR #74)
This is essentially what it used to do. I'm thinking it may be better to just change GS back to what you have here with GCALL as the phred-scaled score may be useful for parsing via bcftools is not actually a good metric for GS.
For the gentrain score, that is encoded in the cluster file (egt) and out of the scope of this tool. This tool may help you out:
https://github.com/Illumina/BeadArrayFiles/blob/develop/examples/locus_summary.py
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@Ahhgust Quick update: I was advised to point you to Illumina's C#/dotnet core implementation of GTCtoVCF here: |
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Thanks!
FYSA, there may be a bug in the current build. See:
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If you look carefully, you'll see that the SampleID is missing.
(This is using version: Array Analysis CLI 2.1.0)
Using the following command:
array-analysis-cli genotype gtc-to-vcf --csv-manifest /eva/edatums/reference_materials/snp_panel_info/GSA/GRCh38/Manifests/GSA-24v3-0_A2.csv --genome-fasta-file /eva/edatums/reference_materials/reference_genomes/grch38/Homo_sapiens.GRCh38.dna.primary_assembly.fa --unsquash-duplicates --gtc-folder GTC --bpm-manifest /eva/edatums/reference_materials/snp_panel_info/GSA/GRCh38/Manifests/GSA-24v3-0_A2.bpm --output-folder VCFs/
…-August
From: jzieve ***@***.***>
Sent: Friday, May 5, 2023 1:06 PM
To: Illumina/GTCtoVCF ***@***.***>
Cc: Woerner, August ***@***.***>; Mention ***@***.***>
Subject: [EXT] Re: [Illumina/GTCtoVCF] Now supports extracting gencall scores (GCALL) as real numbers (PR #74)
@Ahhgust<https://github.com/Ahhgust> Quick update: I was advised to point you to Illumina's C#/dotnet core implementation of GTCtoVCF here:
https://support.illumina.com/array/array_software/ima-array-analysis-cli.html (i.e. see latest README about semi-archived state).
The 2.0 version of that software should reflect the GS score as you prefer (i.e. not phred-scaled).
Hopefully that helps meet your needs.
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Thanks for bringing to my attention. But sorry not following... did you paste something? Where is the SampleID missing? |
I added support for exporting an extra field; the GenCall score (without Phred scaling, so as to have better precision).
(And I use git forking mechanics once in a blue moon, so apologies in advance!)
While this is not the place, it would also be handy to export the gentrain score too, but I could not find programmatic access to it.
Thanks!
-August