how to get hla_gen.format.filter.extend.DRB.no26789.fasta ?

[lidd77]

Hello,
could you tell us how to get this ref file , hla_gen.format.filter.extend.DRB.no26789.fasta ?
I checked this fasta , for example , it is only 2-field fasta sequence . so how to get 2-filed allele sequence from IMGT ?
I find IMGT is full resolution sequence database ( 4-field).
Expecting your repley !

thank you !

[wshuai294]

Hi, to reduce computational resources, we only keep one allele at the 2-field resolution in the read binning step.

[lidd77]

Hi, to reduce computational resources, we only keep one allele at the 2-field resolution in the read binning step.

thank you for your reply ! could you send me some scripts to build this fasta reference ?

[wshuai294]

The script to generate the reference is not kept. You can just retain one allele for each group of alleles with the same two-field type. Also, you can simply keep all the alleles.

[lidd77]

The script to generate the reference is not kept. You can just retain one allele for each group of alleles with the same two-field type. Also, you can simply keep all the alleles.

Hello,
I find this file hla_gen.format.filter.extend.DRB.no26789.fasta don't update its allele list against IMGT3.39 .
for example,
the next list is in hla_gen.format.filter.extend.DRB.no26789.fasta .

DQB102:01
DQB102:02
DQB103:01
DQB103:02
DQB103:04
DQB103:05
DQB103:19
DQB104:01
DQB104:02
DQB105:01
DQB105:02
DQB105:03
DQB105:04
DQB106:01
DQB106:02
DQB106:03
DQB106:04
DQB106:07
DQB106:08
DQB106:09
DQB106:10
DQB106:11
DQB106:14
DQB106:20

but I check DQB1 in IMGTHLA-3.39.0-alpha/fasta/DQB1_gen.fasta and find so many alleles not in that file .
for example, these below alleles not in hla_gen.format.filter.extend.DRB.no26789.fasta.

HLA:HLA06518 DQB106:44 6373 bp
HLA:HLA06877 DQB106:46 6700 bp
HLA:HLA07539 DQB106:48:01 6561 bp
HLA:HLA07820 DQB106:49 6671 bp
HLA:HLA09472 DQB106:84 7102 bp
HLA:HLA09733 DQB106:90 7103 bp

this situation will cause that specHLA miss some allele typing ?

Expecting your reply !

@wshuai294

[wshuai294]

Please have a look at the manuscript for this part.