hi,
For some of the imputed markers, the genomic positions in the markers' names are different than the position provided by the imputation result. for example:
Part of The imputation result:
CHR POS ID REF ALT
6 29910961 SNPS_A_387_29910717_exon2_A A T
6 29910962 SNPS_A_387_29910717_exon2_G A T
6 29910963 SNPS_A_387_29910717_exon2_T A T
6 29910978 SNPS_A_395_29910725_exon2_C A T
6 29910979 SNPS_A_395_29910725_exon2_G A T
6 29910389 AAA-15_29910359_exon1_V A T
6 29910391 AAA-11_29910371_exon1_S A T
6 32551533 AA_DRB1_96_32549647_exon3_H A T
6 32551534 AA_DRB1_96_32549647_exon3_HI A T
6 32551536 AA_DRB1_96_32549647_exon3_HIQ A T
According to the HLA imputation pipeline on the Michigan Imputation Server, the interpretation of the imputed markers are:
AA[GENE][AMINO ACID POSITION][GENOMIC POSITION][EXON][RESIDUE]
SNPS[GENE][GENE POSITION][GENOMIC POSITION]_[EXON/INTRON]
As you can see, the POS of the markers are not the same of the GENOMIC POSITION. In addition, all the amino acid markers have A/T as REF/ALT. And does the residue indicates the original amino acid residue or the amino acid after change?
hi, For some of the imputed markers, the genomic positions in the markers' names are different than the position provided by the imputation result. for example: Part of The imputation result: CHR POS ID REF ALT 6 29910961 SNPS_A_387_29910717_exon2_A A T 6 29910962 SNPS_A_387_29910717_exon2_G A T 6 29910963 SNPS_A_387_29910717_exon2_T A T 6 29910978 SNPS_A_395_29910725_exon2_C A T 6 29910979 SNPS_A_395_29910725_exon2_G A T 6 29910389 AAA-15_29910359_exon1_V A T 6 29910391 AAA-11_29910371_exon1_S A T 6 32551533 AA_DRB1_96_32549647_exon3_H A T 6 32551534 AA_DRB1_96_32549647_exon3_HI A T 6 32551536 AA_DRB1_96_32549647_exon3_HIQ A T
According to the HLA imputation pipeline on the Michigan Imputation Server, the interpretation of the imputed markers are: AA[GENE][AMINO ACID POSITION][GENOMIC POSITION][EXON][RESIDUE] SNPS[GENE][GENE POSITION][GENOMIC POSITION]_[EXON/INTRON]
As you can see, the POS of the markers are not the same of the GENOMIC POSITION. In addition, all the amino acid markers have A/T as REF/ALT. And does the residue indicates the original amino acid residue or the amino acid after change?
Thank you!