Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
I'm trying to use the pre-imputation checks here https://www.well.ox.ac.uk/~wrayner/tools/ to check a vcf (on the hg38 assembly) on the 1000G phase 3 v5 data, which is hg19, before imputing using the MIS.
I am trying to use 1000G phase3 V5 reference to impute my hg38 genotype data. I am trying to run
perl HRC-1000G-check-bim.pl \ -b chr1.bim \ -f chr1.freq.frq \ -r 1000GP_Phase3_combined.legend \ -g -p EUR \
Which is not working since mismatch between input and ref version.
May I know if I need to liftover my data to hg19 for purpose of doing imputation in Michigan imputation server.
Please help. thanks.
• 982 views
•
link
updated
by
bk11 •
•
written
by
guoweidora •
•
written
by
guoweidora •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Imputation advice
written by kl •
-
No valid chromosomes found! on Michigan Imputation Server
written by graeme.thorn
-
Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
written by graeme.thorn
-
Can't liftover vcf file from hg19 to hg38
written by Victor •
-
Discrepancy between genotype and reference genome build - issue with strand flips
written by dam4l
-
PCA results shows mixed population ?
written by putty •
-
pre-imputation allele frequency check against HRC reference panel
written by psb7 •
-
Why does genotype data change after genetic imputation?
written by iamselewa •
-
Allele frequencies not matching with reference panel (HRC)
written by ZB •
-
Low SNP imputation concordance - except chromosome 1
written by muraved •
Basically, you necessarily do not have to liftover your data to hg19 from hg38. You can do pre-imputation QC using TOPMed reference data instead which in hg38.