Hi,
we obtained our data from SNP genotyping from external lab. We found out, that there are letters "'D" and "I" in some positions. Do you know what those means? It is also in the reference fields.
example:
1 13901895 chr1_13901894 D I
1 13903334 chr1_13903333 I D
1 13903422 chr1_13903421 I .
Thank you very much for your help.
Jochen Wilhelm I think that too but it is wierd that it is also in the reference genome file from which the reference alleles were obtained. To have a deletion as a reference state in the genome is kind of wierd. :/ But I obtained those data as it is.
I am having trouble to submit this dataset to EVA, that is why I am trying to find out more.
Check out our hands-on workshops in NGS data analysis: https://www.ecseq.com/workshops/ngs-data-analysis-courses
I and D are used for Insertion/Deletions on Illumina arrays. If you know which array was used you can look up in the array manifest the actual alleles being used for the probes - they are in square brackets in the TopGenomicSeq field.
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