HLA--polysolver

文章来自：Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747795/

使用全外显子组测序（WES）检测HLA基因中的体细胞突变受到HLA基因座的高度多态性的阻碍。描述一种计算管道，其能够准确推断I类HLA-A，-B和-C基因的种系等位基因，并使用推断的等位基因作为参考随后检测这些基因中的突变。

A：polysolver算法概要
比对：Novoalign，基于IMGT数据库，加上2步基于贝叶斯的可能性计算
B：与其他算法的性能比较
总平均灵敏度达到97％，总平均精度为98.8％，平均总体准确度为97％，100％纯合子成功率。优于其他4种，与OptiType性能相当。

(i) ethnicity detection using the normal sample;
(ii) inference of HLA type by applying POLYSOLVER on the normal sample (although other highly accurate HLA typing tools could also be used);
(iii) re-alignment of the HLA reads in both tumor and normal to the inferred HLA alleles while filtering out likely erroneous alignments (Online methods);
(iv) application of standard tools to detect somatic mutations (MuTect and Strelka) by comparing the re-aligned tumor and normal HLA reads.

软件下载安装：https://github.com/jason-weirather/hla-polysolver
测试命令（需肿瘤样本和正常样本）：
1.shell_call_hla_type test/test.bam Unknown 1 hg19 STDFQ 0 output（只做HLA，做这一步就可以）
2.shell_call_hla_mutations_from_type test/test.bam test/test.tumor.bam output/winners.hla.txt hg19 STDFQ output
3.shell_annotate_hla_mutations indiv output
Output:
winners.hla.txt: file containing the two inferred alleles for each of HLA-A, HLA-B and HLA-C

简单总结：hla-polysolver相对optitype的分辨率高，但是准确率差一些

补充：
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2239-6