Specifications

File format

Genotype format

CSV

• ID: a(ny) unique identifier within the file
• GL-STRING: a GL-String per the GL String Manuscript
• POP_i: one or more population identifiers. ',' delimits (up to) two lists ';' delimits the list

ID,GL-STRING,POP1;POP2;POP3,POP4

This is an individual with two population identity strings:

• one is a mix of POP1, POP2 and POP3
• the other is POP4

Example:

355310045,A*33:03+A*68:01^B*50:01+B*57:04^C*06:02+C*18:01^DRB1*01:02+DRB1*13:02,AAFA,AAFA

HPF format

CSV

• haplotype: HLA haplotype delimited with "~" in GL-String format
• population: A population identifier
• frequency: Floating point number

H,P,F

Example:

A*24:07~C*04:01~B*35:05~DRB3*03:01~DRB1*12:02~DQB1*03:01,FILII,0.04079961611346017 A*24:02~C*07:02~B*38:02~DRB5*01:01~DRB1*15:02~DQB1*05:02,FILII,0.034274561754028245 A*34:01~C*15:02~B*40:02~DRB5*01:01~DRB1*15:02~DQB1*05:02,FILII,0.027284337715666348

Metadata

Genotype

Metadata for the genotyping

GT_M_TYPE	GT_M_VALUE	DESCRIPTION
TYPING_METHOD	SSO, SSP, Serology, SangerSequencing, NGS, Free Text	The Typing Method used
TYPING_REF	String	A reference to the typing method
TYPING_DATE	Date	Date of typing
TYPING_IPD_IMGT_HLA_DATABASE_VERSION	String	Version of IPD-IMGT-HLA database used
MIRING_REF	Reference	A reference to a MIRING compliant set of details to the typing of the sample

HF Estimation Method

Metadata method used to estimate haplotype frequencies

METH_TYPE	VALUE	DESCRIPTION
EM_ALGORITHM	String	The EM method used
EM_VERSION	String	Version of EM method
EM_ALGORITHM_REF	Reference	A reference to the EM algorithm used
MAC_METHOD
ARS_METHOD
HWE_METHOD
LD_METHOD
EM_PARAMETERS
ARS_PARAMETERS
HWE_PARAMETERS