Different NA12892 HLA results from tutorial

[Tesson98]

Hi @chbe-helix，

I hope this find you well.
When trying to repeat the tutorial HLA typing results with ILMN/NA12892 sample, I got the outputfile named "assembly_graph-hla.NA12892_extracted_1_fq_gz-hla-extracted-1_fq.report" and the output was as follows, which was diffrent from tutorials (https://daehwankimlab.github.io/hisat-genotype/tutorials/#interpreting-output) but the same as results mentioned in issues #11:

`

    # VERSIONS:
    # HISAT2 - 2.2.1
    # HISAT-genotype - 1.3.2
    # Database - Database /dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/indicies/hla derived from HISATgenotype DB version: NONE
    # COMMAND:/dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/hisatgenotype --base hla --locus-list A -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz --threads 16

	hisat2 graph
		1496 reads and 769 pairs are aligned
			1 A*02:01:01:01 (count: 419)
			2 A*02:251 (count: 407)
			3 A*02:610:02 (count: 405)
			4 A*02:524:02 (count: 403)
			5 A*02:650 (count: 403)
			6 A*02:01:123 (count: 402)
			7 A*02:647 (count: 401)
			8 A*02:01:126 (count: 400)
			9 A*02:562 (count: 400)
			10 A*02:645 (count: 400)


			1 ranked A*02:01:01:01 (abundance: 51.95%)
			2 ranked A*11:01:01:01 (abundance: 48.05%)

`

Was my output correct?

Thank you so much!

Tesson,
2024.10.19

[Tesson98]

Additional,
If I tried to do MHC-I and MHC-II genotyping with ILMN/NA12892 sample, I got 100% abudance in DQB1 and DRB1 allele genes. For those genes, should I directly treated them as homozygous? For example, if I get "1 ranked DRB101:01:01 (abundance: 100.00%)" and "1 ranked DQB105:01:01:03 (abundance: 100.00%)", the DRB1 and DQB1 genotypes of this sample were DRB101:01:01-DRB101:01:01 and DQB105:01:01:03-DQB105:01:01:03 ?
The output was as follows:
`

    # VERSIONS:
     # HISAT2 - 2.2.1
     # HISAT-genotype - 1.3.2
     # Database - Database /dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/indicies/hla derived from HISATgenotype DB version: NONE
     # COMMAND:/dssg/home/acct-medzwli/medzwli/Tesson_main/Softwares/hisatgenotype/hisatgenotype --base hla -v --locus-list A,B,C,DPA1,DPB1,DPB2,DQA1,DQB1,DRA,DRB1,DRB5 -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz --out-dir out

	hisat2 graph
		4377 reads and 2247 pairs are aligned
			1 DPA1*01:03:01:03 (count: 1556)
			2 DPA1*01:03:01:02 (count: 1536)
			3 DPA1*02:01:01:02 (count: 1497)
			4 DPA1*01:03:01:04 (count: 1482)
			5 DPA1*02:01:01:01 (count: 1438)
			6 DPA1*02:01:08 (count: 1395)
			7 DPA1*01:03:01:05 (count: 1386)
			8 DPA1*02:01:02 (count: 1372)
			9 DPA1*01:03:01:01 (count: 1337)
			10 DPA1*01:03:05 (count: 1320)


			1 ranked DPA1*02:01:01:02 (abundance: 52.97%)
			2 ranked DPA1*01:03:01:01 (abundance: 34.00%)
			3 ranked DPA1*02:01:01:01 (abundance: 7.80%)
			4 ranked DPA1*01:03:01:03 (abundance: 5.24%)
		5901 reads and 2987 pairs are aligned
			1 DPB1*03:01:01 (count: 2654)
			2 DPB1*45:01 (count: 2599)
			3 DPB1*104:01 (count: 2177)
			4 DPB1*16:01:01 (count: 2139)
			5 DPB1*463:01 (count: 2120)
			6 DPB1*584:01 (count: 1676)
			7 DPB1*40:01 (count: 1100)
			8 DPB1*398:01 (count: 889)
			9 DPB1*04:01:31 (count: 878)
			10 DPB1*04:01:01:01 (count: 877)


			1 ranked DPB1*06:01:01 (abundance: 50.56%)
			2 ranked DPB1*14:01:01 (abundance: 49.44%)
		9389 reads and 4743 pairs are aligned
			1 DPB2*01:01:01 (count: 3670)
			2 DPB2*03:01:01:03 (count: 2878)
			3 DPB2*02:01 (count: 2578)
			4 DPB2*03:01:01:01 (count: 2266)
			5 DPB2*03:01:01:02 (count: 2238)
			6 DPB2*01:01:02 (count: 1970)


			1 ranked DPB2*01:01:01 (abundance: 69.06%)
			2 ranked DPB2*01:01:02 (abundance: 22.72%)
			3 ranked DPB2*03:01:01:01 (abundance: 4.50%)
			4 ranked DPB2*03:01:01:02 (abundance: 3.72%)
		3313 reads and 1681 pairs are aligned
			1 DQA1*01:01:02 (count: 1458)
			2 DQA1*01:01:01:03 (count: 1432)
			3 DQA1*01:01:01:01 (count: 1401)
			4 DQA1*01:01:01:02 (count: 1390)
			5 DQA1*01:05:01 (count: 743)
			6 DQA1*01:04:01:02 (count: 729)
			7 DQA1*01:04:01:01 (count: 728)
			8 DQA1*01:04:01:04 (count: 665)
			9 DQA1*01:07Q (count: 664)
			10 DQA1*01:04:01:03 (count: 654)


			1 ranked DQA1*01:01:01:03 (abundance: 76.27%)
			2 ranked DQA1*01:01:01:01 (abundance: 23.73%)
		3547 reads and 1795 pairs are aligned
			1 DQB1*05:01:01:03 (count: 1795)
			2 DQB1*05:103 (count: 1748)
			3 DQB1*05:01:01:02 (count: 1746)
			4 DQB1*05:104 (count: 1744)
			5 DQB1*05:01:01:01 (count: 1681)
			6 DQB1*05:52 (count: 1027)
			7 DQB1*05:02:01 (count: 1010)
			8 DQB1*05:97 (count: 1010)
			9 DQB1*05:03:01:01 (count: 1009)
			10 DQB1*05:106 (count: 996)


			1 ranked DQB1*05:01:01:03 (abundance: 100.00%)
		3048 reads and 1532 pairs are aligned
			1 DRA*01:01:02 (count: 1007)
			2 DRA*01:02:01 (count: 904)
			3 DRA*01:02:02 (count: 886)
			4 DRA*01:01:01:02 (count: 802)
			5 DRA*01:01:01:03 (count: 790)
			6 DRA*01:01:01:01 (count: 742)
			7 DRA*01:02:03 (count: 616)


			1 ranked DRA*01:02:01 (abundance: 69.11%)
			2 ranked DRA*01:01:02 (abundance: 30.89%)
		5514 reads and 2794 pairs are aligned
			1 DRB1*01:01:01 (count: 2746)
			2 DRB1*01:02:01 (count: 2561)
			3 DRB1*01:03 (count: 2301)
			4 DRB1*12:17 (count: 1717)
			5 DRB1*16:01:01 (count: 408)
			6 DRB1*16:02:01:02 (count: 408)
			7 DRB1*16:02:01:01 (count: 360)
			8 DRB1*15:02:01:02 (count: 300)
			9 DRB1*15:02:01:01 (count: 298)
			10 DRB1*15:01:01:02 (count: 240)


			1 ranked DRB1*01:01:01 (abundance: 100.00%)

`
Thanks again and hope for your reply!