Imputation results from TOPMED server

Question

[mel22]

Hello, I used the TOPMED imputation server to impute my data, originally Grch37. As explained the server update the data to Grch38 and impute The results are without any RS ID , the names are the position -1 (below), is this accespted result or there is an error ?

Thank you very much for your help !

Results example :

Variant Location Allele
chr1:109080933:A:G 1:109080934-109080934 G
chr10:22529849:G:A 10:22529850-22529850 A
chr10:22529932:T:C 10:22529933-22529933 C

[Nicolas Rosewick]

what do you mean by "the names are the position + 1" ? Could you post one line of the resulting imputed vcf. To annotate the imputed vcf you should use dbsnp hg38 vcf with bcftools annotate

[mel22]

Hi Nicolas, For example the first line the variant is chr1:109080933:A:G and the position is 1:109080934-109080934.

The VCF file :

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

chr22 10522162 chr22:10522162:G:A G A . PASS AF=0.00001;MAF=0.00001;R2=0.00115;IMPUTED GT:DS:HDS:GP

Thank you very much !

[Nicolas Rosewick]

chr1:109080933:A:G seems correct looking at gnomAD : https://gnomad.broadinstitute.org/variant/1-109080933-A-G?dataset=gnomad_r3 . Where did you find the position 1:109080934-109080934. . Also vcf line seems fine for me.

[mel22]

When I tried to annotate with VEP tool ( ensembl) it add 1 automatically for each position, so i thought it could be an imputation error ....