发现这个软件之前的官网已经打不开，但是在github上仍然在更新，https://github.com/SyntekabioTools/HLAscan或许是换了工作？最近一次更新是2019.12.4，还是比较新的。发现wegene的NGS HLA分型报告是用的这个软件的参考文献，估计还是权威些的。

软件使用方法也有了一些变化，之前只是一个脚本，现在直接编译成了一个独立的可执行文件，运行效率应该也有很大的提高。也省去安装的繁琐。AMD YES的4700U也能跑得动，不错！

安装和运行

# 下载软件 wget https://github.com/SyntekabioTools/HLAscan/releases/download/v2.1.4/hla_scan_r_v2.1.4 wget https://github.com/SyntekabioTools/HLAscan/releases/download/v2.0.0/dataset.zip #解压 unzip dataset.zip #循环运行分型数据 for gene in HLA-A HLA-B HLA-C HLA-E HLA-F HLA-G MICA MICB HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB5 TAP1 TAP2 do ./hla_scan_r_v2.1.4 -l ../read_1.fq -r ../read_2.fq -d db/HLA-ALL.IMGT -t 8 -g $gene done

结果

然后就有了结果呀。

===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:4:15 ======================================================== HLA gene : HLA-A # of considered types : 3182 ----------- HLA-Types ----------- [Type 1] 31:01:02:01 EX3_209.094_100 EX2_244.789_100 EX4_291.888_100 EX5_190.632_100 [Type 2] 03:01:01:03 EX3_166.42_100 EX2_197.259_100 EX4_250.399_100 EX5_169.726_100 ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:13:32 ======================================================== HLA gene : HLA-B # of considered types : 3958 ----------- HLA-Types ----------- [Type 1] 48:01:01 EX3_528.214_100 EX2_654.385_100 EX4_984.435_100 EX5_607.077_100 [Type 2] 15:11:01 EX3_368.938_100 EX2_464.43_100 EX4_692.304_100 EX5_423.094_100 ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:20:25 ======================================================== HLA gene : HLA-C # of considered types : 2735 ----------- HLA-Types ----------- [Type 1] 08:01:01 EX3_169.279_100 EX2_194.726_100 EX4_296.558_100 EX5_194.783_100 [Type 2] 03:03:01 EX3_167.344_100 EX2_171.144_100 EX4_266.931_100 EX5_155.4_100 ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:20:28 ======================================================== HLA gene : HLA-E # of considered types : 17 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:20:32 ======================================================== HLA gene : HLA-F # of considered types : 22 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:20:40 ======================================================== HLA gene : HLA-G # of considered types : 50 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:20:57 ======================================================== HLA gene : MICA # of considered types : 102 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:21:3 ======================================================== HLA gene : MICB # of considered types : 41 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:21:4 ======================================================== HLA gene : HLA-DMA # of considered types : 7 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:21:6 ======================================================== HLA gene : HLA-DMB # of considered types : 13 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:21:8 ======================================================== HLA gene : HLA-DOA # of considered types : 12 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:21:10 ======================================================== HLA gene : HLA-DOB # of considered types : 13 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:21:16 ======================================================== HLA gene : HLA-DPA1 # of considered types : 40 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:22:30 ======================================================== HLA gene : HLA-DPB1 # of considered types : 550 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:22:37 ======================================================== HLA gene : HLA-DQA1 # of considered types : 54 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:24:20 ======================================================== HLA gene : HLA-DQB1 # of considered types : 806 ----------- HLA-Types ----------- [Type 1] 03:03:02:01 EX2_380.615_100 EX3_638.819_100 EX4_0_0 [Type 2] 06:02:01 EX2_285.522_100 EX3_589.078_100 EX4_0_0 ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:24:21 ======================================================== HLA gene : HLA-DRA # of considered types : 7 ----------- HLA-Types ----------- HLAscan cannot determine proper types ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:28:15 ======================================================== HLA gene : HLA-DRB1 # of considered types : 1756 ----------- HLA-Types ----------- [Type 1] 09:01:02 EX2_791.144_100 EX3_672.496_100 EX4_0_0 [Type 2] 15:01:01:04 EX2_707.333_100 EX3_651.83_100 EX4_0_0 ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:28:18 ======================================================== HLA gene : HLA-DRB5 # of considered types : 21 ----------- HLA-Types ----------- [Type 1] 02:06 EX2_14.9259_50 EX3_0.58156_0 EX4_0_0 [Type 2] 02:06 EX2_14.9259_50 EX3_0.58156_0 EX4_0_0 ===================================================== HLAscan v2.1 Report created 2020. 10. 21. 12:28:20 ========================================================