Allele frequencies not matching with reference panel (HRC)
Please share your thoughts about possible reasons and any solutions?
I am replicating data from this paper
McLaren et al. 2015. Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load.PNAS.112(47):14658–14663.
The log file of pre-imputation steps was generated using this command
perl <HRC-1000G-check-bim.pl> -b <data.chr1.bim> -f <data.chr1.frq> -r <reference i.e. HRC.r1-1.GRCh37.wgs.mac5.sites.vcf.gz> -h
(screen shot attached) and unusually large number of SNPs were removed. The frequencies on reference panel and my data were not matching. What could be the reason?
Any solution to rectify the error?
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