However, some aspects of the results are very confusing to me. Perhaps see #3 (the most confusing) first.
- There are 62,623 rsIDs for chromosome 3 in my 23andMe file and 2,821,894 SNPs (actually, unique rsIDs) after imputation. However, only 60,144 of the original 62,623 rsIDs are in that ~2.8 million. Where did the other 2,479 go? Here are some examples of missing rsIDs: rs1516332, rs12374025, rs1170695, rs2731343 and rs63749864.
EDIT Point 1
rs1516332, the position is 3:105793, which does have a result in the file, but it doesn't have an rsID:
3 105793 . C T . PASS RefPanelAF=0.17878;AN=2;AC=0;INFO=1 GT:ADS:DS:GP 0|0:0,0:0:1,0,0
rs63749864 (3:13564048) it's missing by rsID and position.
EDIT Point 1 (again)
As described here: https://github.com/richarddurbin/pbwt/issues/51
"... of the 2,479 'missing' SNPs, 1,806 can be 'found' [by position] leaving 673 'anchors' [or rsIDs called by 23andMe] missing from chromosome 3."
- Some imputed rsIDs appear more than once in the results. How should I interpret that? e.g.
3 64071 rs116059446 G T . PASS RefPanelAF=0.000369572;AN=2;AC=0;INFO=1 GT:ADS:DS:GP 0|0:0,0:0:1,0,0 3 64071 rs116059446 G A . PASS RefPanelAF=9.2393e-05;AN=2;AC=0;INFO=1 GT:ADS:DS:GP 0|0:0,0:0:1,0,0
EDIT Point 2 From the answer below, this is a variant with more than two alleles: rs116059446
Seems the format of this VCF file only allows one alt per line, hence the two alts are split over two lines.
See my question here: Is it valid VCF not to 'squash' positions with more than one ALT allele?
And the answer from Durbo here: https://github.com/richarddurbin/pbwt/issues/52#issuecomment-1062951105
In the above case, the genotype is easy to interpret (REF/REF in both lines).
However, I'm now finding examples that I just can't interpret:
3 255395 rs331869 C G . PASS RefPanelAF=0.385864;AN=2;AC=1;INFO=1 GT:ADS:DS:GP 1|0:1,0:1:0,1,0 3 255395 rs331869 C T . PASS RefPanelAF=0.980998;AN=2;AC=2;INFO=1 GT:ADS:DS:GP 1|1:1,1:2:0,0,1
Is my genotype CG or TT at this position?
- Sometimes a rsID appears twice but at different locations:
3 4942430 rs71634747 G A . PASS RefPanelAF=0.445673;AN=2;AC=1;INFO=1 GT:ADS:DS:GP 1|0:1,0:1:0,1,0 3 4942432 rs71634747 C G . PASS RefPanelAF=0.248907;AN=2;AC=0;INFO=1 GT:ADS:DS:GP 0|0:0,0:0:1,0,0
Unless I'm really confused, this just seems wrong. If it wasn't for this weirdness, I'd seek concrete answers for #1 and #2, but it could be that they are both just a symptom of this potential error?