I am working on some older genotype data (on the PsychChip) where the IDAT files have unfortunately been lost to time, but where we do have a reasonably rich GenomeStudio text format export, and the original csv manifest file used when generating the export. I want to combine this with newer genotyping waves where we do have the IDATs, and would like to remap the markers using gtc2vcf to hopefully be done with strand and allele issues once and for all. But currently gtc2vcf does not permit --genome-studio to be used with --csv and/or --sam-flank.
Would it be possible to extend gtc2vcf to this use case, or is there some vital information I am missing that makes it a bad idea or impossible?
The GS export has columns (followed by 6-15 repeated for each sample):
1: Index
2: Name
3: Address
4: Chr
5: Position
6: S1.GType
7: S1.Score
8: S1.Theta
9: S1.R
10: S1.X Raw
11: S1.Y Raw
12: S1.X
13: S1.Y
14: S1.B Allele Freq
15: S1.Log R Ratio
16: ...
Hello, and thanks for a great tool!
I am working on some older genotype data (on the PsychChip) where the IDAT files have unfortunately been lost to time, but where we do have a reasonably rich GenomeStudio text format export, and the original csv manifest file used when generating the export. I want to combine this with newer genotyping waves where we do have the IDATs, and would like to remap the markers using gtc2vcf to hopefully be done with strand and allele issues once and for all. But currently gtc2vcf does not permit --genome-studio to be used with --csv and/or --sam-flank.
Would it be possible to extend gtc2vcf to this use case, or is there some vital information I am missing that makes it a bad idea or impossible?
The GS export has columns (followed by 6-15 repeated for each sample):
My csv manifest has columns: