Hello,
I noticed there are many cases of different variants at the same position, such as:
22 chr22:50473781:IG 0 50473781 T TC
22 chr22:50473781:SG 0 50473781 A T
these 2 have same position, but different alleles, and different IDs. What do "IG", "IG0" and "SG" stand for? I need to match WGS with imputed data, which only have one identifier per position, in the form of chrx:position, so it gets a bit tricky and it would be useful to know if I can prioritize one of these duplicates.
Thanks
I'm not sure about designation of "IG", "IG0" and "SG". I would guess IG is insertion of something and SG is SNPs of something. You can contact UKB directly that you need more documentation for this data.
How would you match the variants from different data processing is a research question and also depend on what you plan to do with the matching.
How I understand this - for different variation type (e.g. snp, indel) at the same location, each variation type is being assigned its own variant/line in VCF file. As @Chai Fungtammasan? said, it really seems that SG stands for substitution and IG stands for indel as this notation is not unusual in variant calling: https://www.strand-ngs.com/files/DNA-variant-analysis.pdf (see Table A)
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I'm not sure about designation of "IG", "IG0" and "SG". I would guess IG is insertion of something and SG is SNPs of something. You can contact UKB directly that you need more documentation for this data.
How would you match the variants from different data processing is a research question and also depend on what you plan to do with the matching.
Thanks, I will contact them directly.
How I understand this - for different variation type (e.g. snp, indel) at the same location, each variation type is being assigned its own variant/line in VCF file. As @Chai Fungtammasan? said, it really seems that SG stands for substitution and IG stands for indel as this notation is not unusual in variant calling: https://www.strand-ngs.com/files/DNA-variant-analysis.pdf (see Table A)
Thanks Ondrej. It is intuitive but I wanted some official source confirming it. Thank you for the link you shared.
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