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HLA NGS数据分析

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发表于 2017-9-21 08:55:42 | 显示全部楼层 |阅读模式
首先是拿到fastq文件,然后进行了下fastqc质控,发现质量不咋地,死马当活马医,试试。然后是bwa比对,先是
bwa index /home/biolinux/reference/hg38.fa #建立索引bwa mem /home/biolinux/reference/hg38.fa /home/biolinux/Downloads/HLA.fastq > hla.sam #然后比对samtools view -S hla.sam -b > hla.bam #格式转换samtools sort hla.bam hla_sorted.bam # 排序samtools index hla_sorted.bam # 索引
最后,进行xhla算法比对。
docker run -v `pwd`:`pwd` -w `pwd` humanlongevity/hla --sample_id test --input_bam_path hla.bam --output_path test
得出结果,一个比较疑惑的地方是hg38(without alt contigs)没搞懂。有待解决。
xHLA is compatible with BAM file against hg38 (no ALT contigs). Supported aligners include:

BWA-mem with default parameter
Illumina Isis/Isaac software
For example, reference sequences in the GATK resource bundle contain HLA contigs that might trap reads in those contigs, instead of in region chr6:29844528-33100696 assumed by xHLA.

For BAMs generated with ALT+HLA contigs or with funny alignment parameters, we need to extract all ALT+HLA+unmapped contigs and re-align with BWA-mem using default parameters.

{ "subject_id": "test",  "creation_time": "2017-09-19T07:09:32Z",  "report_version": "1.2",  "report_type": "hla_typing",  "sample_id": "test",  "hla": {  "alleles": [   "A*24:290",    "A*24:290",    "C*07:02",    "C*07:02",    "DPB1*13:01",    "DPB1*33:01",    "DQB1*06:11",    "DQB1*06:39",    "DRB1*15:01",    "DRB1*16:01"  ] }}




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