Ref/Alt allele mapping


These files are for use in plink with the --reference-allele command, allowing Allele1 to be set to match the reference genome.
NOTE: at the present time the files are not 100% correct for indels, whilst the allele assignment is correct, the allele listed may be truncated.


BDCHP-1X10-HUMANHAP240S_11216501_A
BDCHP-1X10-HUMANHAP240S_11216501_A-b37.strand.RefAlt.zip
BDCHP-1X10-HUMANHAP240S_11216501_A-b38.strand.RefAlt.zip

BDCHP-1x10-HUMANHAP300v1-1_11219278_C
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b37.strand.RefAlt.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b38.strand.RefAlt.zip

BDCHP-1X10-HUMANHAP550_11218540_C
BDCHP-1X10-HUMANHAP550_11218540_C-b37.strand.RefAlt.zip
BDCHP-1X10-HUMANHAP550_11218540_C-b38.strand.RefAlt.zip

Cardio-Metabo_Chip_11395247_A
Cardio-Metabo_Chip_11395247_A-b37.strand.RefAlt.zip
Cardio-Metabo_Chip_11395247_A-b38.strand.RefAlt.zip

cardio-metabo_chip_11395247_c
cardio-metabo_chip_11395247_c-b37.strand.RefAlt.zip
cardio-metabo_chip_11395247_c-b38.strand.RefAlt.zip

CVDSNP55v1_A
CVDSNP55v1_A-b37.strand.RefAlt.zip
CVDSNP55v1_A-b38.strand.RefAlt.zip

cytosnp-850k_b
cytosnp-850k_b-b37.strand.RefAlt.zip
cytosnp-850k_b-b38.strand.RefAlt.zip

Final_custom15K
Final_custom15K-b37.strand.RefAlt.zip
Final_custom15K-b38.strand.RefAlt.zip

Human1-2M-DuoCustom_v1_A
Human1-2M-DuoCustom_v1_A-b37.strand.RefAlt.zip
Human1-2M-DuoCustom_v1_A-b38.strand.RefAlt.zip

Human1M-Duov3_B
Human1M-Duov3_B-b37.strand.RefAlt.zip
Human1M-Duov3_B-b38.strand.RefAlt.zip

Human1M-Duov3_C
Human1M-Duov3_C-b37.strand.RefAlt.zip
Human1M-Duov3_C-b38.strand.RefAlt.zip

human1m-duov3_h
human1m-duov3_h-b37.strand.RefAlt.zip
human1m-duov3_h-b38.strand.RefAlt.zip

Human1Mv1_C
Human1Mv1_C-b37.strand.RefAlt.zip
Human1Mv1_C-b38.strand.RefAlt.zip

Human610-Quadv1_B
Human610-Quadv1_B-b37.strand.RefAlt.zip
Human610-Quadv1_B-b38.strand.RefAlt.zip

human610-quadv1_h
human610-quadv1_h-b37.strand.RefAlt.zip
human610-quadv1_h-b38.strand.RefAlt.zip

Human660W-Quad_v1_A
Human660W-Quad_v1_A-b37.strand.RefAlt.zip
Human660W-Quad_v1_A-b38.strand.RefAlt.zip

Human660W-Quad_v1_C
Human660W-Quad_v1_C-b37.strand.RefAlt.zip
Human660W-Quad_v1_C-b38.strand.RefAlt.zip

human660w-quad_v1_h
human660w-quad_v1_h-b37.strand.RefAlt.zip
human660w-quad_v1_h-b38.strand.RefAlt.zip

Human670-QuadCustom_v1_A
Human670-QuadCustom_v1_A-b37.strand.RefAlt.zip
Human670-QuadCustom_v1_A-b38.strand.RefAlt.zip

HumanCNV370-Quadv3_C
HumanCNV370-Quadv3_C-b37.strand.RefAlt.zip
HumanCNV370-Quadv3_C-b38.strand.RefAlt.zip

HumanCNV370v1_C
HumanCNV370v1_C-b37.strand.RefAlt.zip
HumanCNV370v1_C-b38.strand.RefAlt.zip

humancore-12v1-0_a
humancore-12v1-0_a-b37.strand.RefAlt.zip
humancore-12v1-0_a-b38.strand.RefAlt.zip

humancore-24-v1-0-manifest-file-a
humancore-24-v1-0-manifest-file-a-b37.strand.RefAlt.zip
humancore-24-v1-0-manifest-file-a-b38.strand.RefAlt.zip

HumanCoreExome-12v1-0_B
HumanCoreExome-12v1-0_B-b37.strand.RefAlt.zip
HumanCoreExome-12v1-0_B-b38.strand.RefAlt.zip

humancoreexome-12v1-0_c
humancoreexome-12v1-0_c-b37.strand.RefAlt.zip
humancoreexome-12v1-0_c-b38.strand.RefAlt.zip

humancoreexome-12v1-1_a
humancoreexome-12v1-1_a-b37.strand.RefAlt.zip
humancoreexome-12v1-1_a-b38.strand.RefAlt.zip

HumanCoreExome-12v1-1_B
HumanCoreExome-12v1-1_B-b37.strand.RefAlt.zip
HumanCoreExome-12v1-1_B-b38.strand.RefAlt.zip

HumanCoreExome-24v1-0_A
HumanCoreExome-24v1-0_A-b37.strand.RefAlt.zip
HumanCoreExome-24v1-0_A-b38.strand.RefAlt.zip

HumanCytoSNP-12v1-0_D
HumanCytoSNP-12v1-0_D-b37.strand.RefAlt.zip
HumanCytoSNP-12v1-0_D-b38.strand.RefAlt.zip

humancytosnp-12v2-1_h
humancytosnp-12v2-1_h-b37.strand.RefAlt.zip
humancytosnp-12v2-1_h-b38.strand.RefAlt.zip

humancytosnp-12v2-1_l
humancytosnp-12v2-1_l-b37.strand.RefAlt.zip
humancytosnp-12v2-1_l-b38.strand.RefAlt.zip

humancytosnp-12v2.1-ffpe_g
humancytosnp-12v2.1-ffpe_g-b37.strand.RefAlt.zip
humancytosnp-12v2.1-ffpe_g-b38.strand.RefAlt.zip

HumanCytoSNP-12v2.1-FFPE_G
HumanCytoSNP-12v2.1-FFPE_G-b37.strand.RefAlt.zip
HumanCytoSNP-12v2.1-FFPE_G-b38.strand.RefAlt.zip

humancytosnp-12v2_h
humancytosnp-12v2_h-b37.strand.RefAlt.zip
humancytosnp-12v2_h-b38.strand.RefAlt.zip

HumanExome-12v1-1_A
HumanExome-12v1-1_A-b37.strand.RefAlt.zip
HumanExome-12v1-1_A-b38.strand.RefAlt.zip

humanexome-12v1-1_a
humanexome-12v1-1_a-b37.strand.RefAlt.zip
humanexome-12v1-1_a-b38.strand.RefAlt.zip

HumanExome-12v1-2_A
HumanExome-12v1-2_A-b37.strand.RefAlt.zip
HumanExome-12v1-2_A-b38.strand.RefAlt.zip

HumanExome-12v1_A
HumanExome-12v1_A-b37.strand.RefAlt.zip
HumanExome-12v1_A-b38.strand.RefAlt.zip

humanexome-12v1_a
humanexome-12v1_a-b37.strand.RefAlt.zip
humanexome-12v1_a-b38.strand.RefAlt.zip

HumanHap300v2_A
HumanHap300v2_A-b37.strand.RefAlt.zip
HumanHap300v2_A-b38.strand.RefAlt.zip

HumanHap550-2v3_B
HumanHap550-2v3_B-b37.strand.RefAlt.zip
HumanHap550-2v3_B-b38.strand.RefAlt.zip

HumanHap550v3_A
HumanHap550v3_A-b37.strand.RefAlt.zip
HumanHap550v3_A-b38.strand.RefAlt.zip

HumanHap650Yv3_A
HumanHap650Yv3_A-b37.strand.RefAlt.zip
HumanHap650Yv3_A-b38.strand.RefAlt.zip

humanomni1-quad_v1-0-multi_h
humanomni1-quad_v1-0-multi_h-b37.strand.RefAlt.zip
humanomni1-quad_v1-0-multi_h-b38.strand.RefAlt.zip

HumanOmni1-Quad_v1-0_B
HumanOmni1-Quad_v1-0_B-b37.strand.RefAlt.zip
HumanOmni1-Quad_v1-0_B-b38.strand.RefAlt.zip

HumanOmni1-Quad_v1-0_C
HumanOmni1-Quad_v1-0_C-b37.strand.RefAlt.zip
HumanOmni1-Quad_v1-0_C-b38.strand.RefAlt.zip

HumanOmni1-Quad_v1-0_H
HumanOmni1-Quad_v1-0_H-b37.strand.RefAlt.zip
HumanOmni1-Quad_v1-0_H-b38.strand.RefAlt.zip

humanomni1-quad_v1-0_h
humanomni1-quad_v1-0_h-b37.strand.RefAlt.zip
humanomni1-quad_v1-0_h-b38.strand.RefAlt.zip

humanomni1s-8v1_h
humanomni1s-8v1_h-b37.strand.RefAlt.zip
humanomni1s-8v1_h-b38.strand.RefAlt.zip

HumanOmni1S-8v1_H
HumanOmni1S-8v1_H-b37.strand.RefAlt.zip
HumanOmni1S-8v1_H-b38.strand.RefAlt.zip

HumanOmni2-5-8-v1-2-A
HumanOmni2-5-8-v1-2-A-b37.strand.RefAlt.zip
HumanOmni2-5-8-v1-2-A-b38.strand.RefAlt.zip

HumanOmni2.5-4v1_B
HumanOmni2.5-4v1_B-b37.strand.RefAlt.zip
HumanOmni2.5-4v1_B-b38.strand.RefAlt.zip

HumanOmni2.5-4v1_D
HumanOmni2.5-4v1_D-b37.strand.RefAlt.zip
HumanOmni2.5-4v1_D-b38.strand.RefAlt.zip

humanomni2.5-4v1_h
humanomni2.5-4v1_h-b37.strand.RefAlt.zip
humanomni2.5-4v1_h-b38.strand.RefAlt.zip

HumanOmni2.5-4v1_H
HumanOmni2.5-4v1_H-b37.strand.RefAlt.zip
HumanOmni2.5-4v1_H-b38.strand.RefAlt.zip

HumanOmni2.5-8v1_A
HumanOmni2.5-8v1_A-b37.strand.RefAlt.zip
HumanOmni2.5-8v1_A-b38.strand.RefAlt.zip

HumanOmni2.5-8v1_C
HumanOmni2.5-8v1_C-b37.strand.RefAlt.zip
HumanOmni2.5-8v1_C-b38.strand.RefAlt.zip

humanomni2.5-8v1_c
humanomni2.5-8v1_c-b37.strand.RefAlt.zip
humanomni2.5-8v1_c-b38.strand.RefAlt.zip

HumanOmni2.5S-8v1_B
HumanOmni2.5S-8v1_B-b37.strand.RefAlt.zip
HumanOmni2.5S-8v1_B-b38.strand.RefAlt.zip

HumanOmni25-8v1-1_A
HumanOmni25-8v1-1_A-b37.strand.RefAlt.zip
HumanOmni25-8v1-1_A-b38.strand.RefAlt.zip

humanomni25exome-8v1_a
humanomni25exome-8v1_a-b37.strand.RefAlt.zip
humanomni25exome-8v1_a-b38.strand.RefAlt.zip

HumanOmni25Exome-8v1_A
HumanOmni25Exome-8v1_A-b37.strand.RefAlt.zip
HumanOmni25Exome-8v1_A-b38.strand.RefAlt.zip

humanomni25m-8v1-1_b
humanomni25m-8v1-1_b-b37.strand.RefAlt.zip
humanomni25m-8v1-1_b-b38.strand.RefAlt.zip

HumanOmni25M-8v1-1_B
HumanOmni25M-8v1-1_B-b37.strand.RefAlt.zip
HumanOmni25M-8v1-1_B-b38.strand.RefAlt.zip

HumanOmni5-4v1_B
HumanOmni5-4v1_B-b37.strand.RefAlt.zip
HumanOmni5-4v1_B-b38.strand.RefAlt.zip

humanomni5-4v1_c
humanomni5-4v1_c-b37.strand.RefAlt.zip
humanomni5-4v1_c-b38.strand.RefAlt.zip

HumanOmni5-4v1_C
HumanOmni5-4v1_C-b37.strand.RefAlt.zip
HumanOmni5-4v1_C-b38.strand.RefAlt.zip

HumanOmni5Exome-4v1-1_A
HumanOmni5Exome-4v1-1_A-b37.strand.RefAlt.zip
HumanOmni5Exome-4v1-1_A-b38.strand.RefAlt.zip

HumanOmni5Exome-4v1_A
HumanOmni5Exome-4v1_A-b37.strand.RefAlt.zip
HumanOmni5Exome-4v1_A-b38.strand.RefAlt.zip

humanomni5exome-4v1_a
humanomni5exome-4v1_a-b37.strand.RefAlt.zip
humanomni5exome-4v1_a-b38.strand.RefAlt.zip

humanomniexpress-12v1-1_a
humanomniexpress-12v1-1_a-b37.strand.RefAlt.zip
humanomniexpress-12v1-1_a-b38.strand.RefAlt.zip

HumanOmniExpress-12v1-1_A
HumanOmniExpress-12v1-1_A-b37.strand.RefAlt.zip
HumanOmniExpress-12v1-1_A-b38.strand.RefAlt.zip

HumanOmniExpress-12v1-1_B
HumanOmniExpress-12v1-1_B-b37.strand.RefAlt.zip
HumanOmniExpress-12v1-1_B-b38.strand.RefAlt.zip

humanomniexpress-12v1-1_b
humanomniexpress-12v1-1_b-b37.strand.RefAlt.zip
humanomniexpress-12v1-1_b-b38.strand.RefAlt.zip

HumanOmniExpress-12v1-Multi_B
HumanOmniExpress-12v1-Multi_B-b37.strand.RefAlt.zip
HumanOmniExpress-12v1-Multi_B-b38.strand.RefAlt.zip

HumanOmniExpress-12v1-Multi_C
HumanOmniExpress-12v1-Multi_C-b37.strand.RefAlt.zip
HumanOmniExpress-12v1-Multi_C-b38.strand.RefAlt.zip

HumanOmniExpress-12v1_A
HumanOmniExpress-12v1_A-b37.strand.RefAlt.zip
HumanOmniExpress-12v1_A-b38.strand.RefAlt.zip

HumanOmniExpress-12v1_H
HumanOmniExpress-12v1_H-b37.strand.RefAlt.zip
HumanOmniExpress-12v1_H-b38.strand.RefAlt.zip

HumanOmniExpress-12v1_J
HumanOmniExpress-12v1_J-b37.strand.RefAlt.zip
HumanOmniExpress-12v1_J-b38.strand.RefAlt.zip

humanomniexpress-12v1_j_ffpe
humanomniexpress-12v1_j_ffpe-b37.strand.RefAlt.zip
humanomniexpress-12v1_j_ffpe-b38.strand.RefAlt.zip

humanomniexpress-24v1-0_a
humanomniexpress-24v1-0_a-b37.strand.RefAlt.zip
humanomniexpress-24v1-0_a-b38.strand.RefAlt.zip

HumanOmniExpressExome-8-v1-2-B
HumanOmniExpressExome-8-v1-2-B-b37.strand.RefAlt.zip
HumanOmniExpressExome-8-v1-2-B-b38.strand.RefAlt.zip

humanomniexpressexome-8v1-0_a
humanomniexpressexome-8v1-0_a-b37.strand.RefAlt.zip
humanomniexpressexome-8v1-0_a-b38.strand.RefAlt.zip

HumanOmniExpressExome-8v1-2_A
HumanOmniExpressExome-8v1-2_A-b37.strand.RefAlt.zip
HumanOmniExpressExome-8v1-2_A-b38.strand.RefAlt.zip

HumanOmniExpressExome-8v1_A
HumanOmniExpressExome-8v1_A-b37.strand.RefAlt.zip
HumanOmniExpressExome-8v1_A-b38.strand.RefAlt.zip

humanomniexpressexome8v12a
humanomniexpressexome8v12a-b37.strand.RefAlt.zip
humanomniexpressexome8v12a-b38.strand.RefAlt.zip

humanomnizhonghua-8v1-1_a
humanomnizhonghua-8v1-1_a-b37.strand.RefAlt.zip
humanomnizhonghua-8v1-1_a-b38.strand.RefAlt.zip

humanomnizhonghua-8v1_b
humanomnizhonghua-8v1_b-b37.strand.RefAlt.zip
humanomnizhonghua-8v1_b-b38.strand.RefAlt.zip

HumanOmniZhongHua-8v1_B
HumanOmniZhongHua-8v1_B-b37.strand.RefAlt.zip
HumanOmniZhongHua-8v1_B-b38.strand.RefAlt.zip

immuno_beadchip_11419691_b
immuno_beadchip_11419691_b-b37.strand.RefAlt.zip
immuno_beadchip_11419691_b-b38.strand.RefAlt.zip

Immuno_BeadChip_11419691_B
Immuno_BeadChip_11419691_B-b37.strand.RefAlt.zip
Immuno_BeadChip_11419691_B-b38.strand.RefAlt.zip

InfiniumImmunoArray-24v2-0_A
InfiniumImmunoArray-24v2-0_A.b37.RefAlt.zip
InfiniumImmunoArray-24v2-0_A.b38.RefAlt.zip

MS_Replication_Chip_15037643_A
MS_Replication_Chip_15037643_A-b37.strand.RefAlt.zip
MS_Replication_Chip_15037643_A-b38.strand.RefAlt.zip

NeuroX_15036164_A
NeuroX_15036164_A-b37.strand.RefAlt.zip
NeuroX_15036164_A-b38.strand.RefAlt.zip

OmniExpressExome-8v1-1_A
OmniExpressExome-8v1-1_A-b37.strand.RefAlt.zip
OmniExpressExome-8v1-1_A-b38.strand.RefAlt.zip

omniexpressexome-8v1-1_b
omniexpressexome-8v1-1_b-b37.strand.RefAlt.zip
omniexpressexome-8v1-1_b-b38.strand.RefAlt.zip

OmniExpressExome-8v1-1_B
OmniExpressExome-8v1-1_B-b37.strand.RefAlt.zip
OmniExpressExome-8v1-1_B-b38.strand.RefAlt.zip

OncoArray-500K_B
OncoArray-500K_B-b37.strand.RefAlt.zip
OncoArray-500K_B-b38.strand.RefAlt.zip

PsychArray-B
PsychArray-B-b37.strand.RefAlt.zip
PsychArray-B-b38.strand.RefAlt.zip

PsychArray_A
PsychArray_A-b37.strand.RefAlt.zip
PsychArray_A-b38.strand.RefAlt.zip

PsychChip_15048346_B
PsychChip_15048346_B-b37.strand.RefAlt.zip
PsychChip_15048346_B-b38.strand.RefAlt.zip