I have been using Michigan server to impute HLA variants on Four-digital V2 panel, while I notice that there are some ""duplicated" Amino Acids that only differ with an extra "." , I checked it in the vcf.gz file with an example below.
6 29910732 AA_A_67_29910732exon2. A T . PASS
6 29910853 AA_A_67_29910732exon2.M A T . PASS
6 29910854 AA_A_67_29910732exon2.V A T . PASS
6 29910855 AA_A_67_29910732exon2.x A T . PASS
6 29910856 AA_A_67_29910732_exon2_M A T . PASS
6 29910857 AA_A_67_29910732_exon2_V A T . PASS
6 AA_A_67_29910732exon2. 0 29910732 T A
6 AA_A_67_29910732exon2.E 0 29911059 T A
6 AA_A_67_29910732exon2.M 0 29911061 T A
6 AA_A_67_29910732exon2.V 0 29911062 T A
6 AA_A_67_29910732exon2.x 0 29911065 T A
6 AA_A_67_29910732_exon2_EM 0 29911067 T A
6 AA_A_67_29910732_exon2_EV 0 29911068 T A
6 AA_A_67_29910732_exon2_Ex 0 29911070 T A
6 AA_A_67_29910732_exon2_M 0 29911071 T A
6 AA_A_67_29910732_exon2_MV 0 29911074 T A
6 AA_A_67_29910732_exon2_Mx 0 29911076 T A
6 AA_A_67_29910732_exon2_V 0 29911079 T A
6 AA_A_67_29910732_exon2_Vx 0 29911080 T A
6 AA_A_67_29910732_exon2_x 0 29911082 T A
I'm really confused about this. Are they just simple duplicates? Or is there another explanation? Could you please give me suggestion? Thank you so much!
Hi,
I have been using Michigan server to impute HLA variants on Four-digital V2 panel, while I notice that there are some ""duplicated" Amino Acids that only differ with an extra "." , I checked it in the vcf.gz file with an example below.
6 29910732 AA_A_67_29910732exon2. A T . PASS 6 29910853 AA_A_67_29910732exon2.M A T . PASS 6 29910854 AA_A_67_29910732exon2.V A T . PASS 6 29910855 AA_A_67_29910732exon2.x A T . PASS 6 29910856 AA_A_67_29910732_exon2_M A T . PASS 6 29910857 AA_A_67_29910732_exon2_V A T . PASS
AF=0.00058;MAF=0.00058;R2=0.26863;IMPUTED GT:DS:HDS:GP 0|0:0:0,0:1,0,0 AF=0.14789;MAF=0.14789;R2=0.99169;IMPUTED GT:DS:HDS:GP 0|0:0:0,0:1,0,0 AF=0.85273;MAF=0.14727;R2=0.99495;IMPUTED GT:DS:HDS:GP 1|1:2.000:1.000,1.000:0.000,0.000,1.000 AF=0.00059;MAF=0.00059;R2=0.26606;IMPUTED GT:DS:HDS:GP 0|0:0:0,0:1,0,0 AF=0.14737;MAF=0.14737;R2=0.99398;IMPUTED GT:DS:HDS:GP 0|0:0:0,0:1,0,0 AF=0.85210;MAF=0.14790;R2=0.99156;IMPUTED GT:DS:HDS:GP 1|1:2.000:1.000,1.000:0.000,0.000,1.000
As we can see, the Estimated Alternate Allele for AA_A_67_29910732exon2.V and AA_A_67_29910732_exon2_V are both TT.
I also checked a reference file you pasted in the Issues #15. https://github.com/immunogenomics/HLA-TAPAS/blob/master/resources/wgsMHC.4digit.bglv4.bim (4-digit)
6 AA_A_67_29910732exon2. 0 29910732 T A 6 AA_A_67_29910732exon2.E 0 29911059 T A 6 AA_A_67_29910732exon2.M 0 29911061 T A 6 AA_A_67_29910732exon2.V 0 29911062 T A 6 AA_A_67_29910732exon2.x 0 29911065 T A 6 AA_A_67_29910732_exon2_EM 0 29911067 T A 6 AA_A_67_29910732_exon2_EV 0 29911068 T A 6 AA_A_67_29910732_exon2_Ex 0 29911070 T A 6 AA_A_67_29910732_exon2_M 0 29911071 T A 6 AA_A_67_29910732_exon2_MV 0 29911074 T A 6 AA_A_67_29910732_exon2_Mx 0 29911076 T A 6 AA_A_67_29910732_exon2_V 0 29911079 T A 6 AA_A_67_29910732_exon2_Vx 0 29911080 T A 6 AA_A_67_29910732_exon2_x 0 29911082 T A
I'm really confused about this. Are they just simple duplicates? Or is there another explanation? Could you please give me suggestion? Thank you so much!