ngs进行HLA分型（二）

用户1075469

发布于 2020-11-11 16:07:42

8290

发布于 2020-11-11 16:07:42

HLAscan

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 

=====================================================

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

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原始发表：2020-11-06，如有侵权请联系 cloudcommunity@tencent.com 删除

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