Question: Imputation results from TOPMED server
0
gravatar for melania 2282
11 weeks ago by
melania 228290
melania 228290 wrote:

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

topmed snp imputation • 200 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by melania 228290
1

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

ADD REPLYlink written 11 weeks ago by Nicolas Rosewick9.2k

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 !

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by melania 228290
1

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.

ADD REPLYlink written 11 weeks ago by Nicolas Rosewick9.2k

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 ....

ADD REPLYlink written 11 weeks ago by melania 228290
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