SNP分析中报错怎么解决

今天小编给大家分享一下SNP分析中报错怎么解决的相关知识点，内容详细，逻辑清晰，相信大部分人都还太了解这方面的知识，所以分享这篇文章给大家参考一下，希望大家阅读完这篇文章后有所收获，下面我们一起来了解一下吧。

SNP分析过程中，由于基因组序列长度过长，会导致GATK软件报错。如下所以：

Exception in thread "main" htsjdk.samtools.SAMException: Exception when processing alignment for BAM index A00253:355:H75GLDSX2:2:1334:20989:8625 1/2 150b aligned read.        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:124)        at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:177)        at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:298)        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)        at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)Caused by: htsjdk.samtools.SAMException: Exception creating BAM index for record A00253:355:H75GLDSX2:2:1334:20989:8625 1/2 150b aligned read.        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:91)        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:121)        ... 4 moreCaused by: java.lang.ArrayIndexOutOfBoundsException: 32770        at htsjdk.samtools.BinningIndexBuilder.processFeature(BinningIndexBuilder.java:136)        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:194)        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:89)        ... 5 more

可以在运行时加入--create-output-bam-index false 选项，不让它创建bam文件的索引文件。

/share/work/biosoft/GATK/gatk-4.2.2.0/gatk --java-options "-XX:ParallelGCThreads=5 -Xmx50g " SplitNCigarReads -R /share/work/database/ref/Triticum_aestivum/IWGSC_v2.1/iwgsc_refseqv2.1_gene_annotation_200916/iwgsc_refseqv2.1_assembly.fa -I /share/nas1/renzx/project/zx-20210524-20_BSR_2xiaomai/ref/ann/9.SNP_Analysis/2.bam_process/CH.bam.dedupped.bam -O /share/nas1/renzx/project/zx-20210524-20_BSR_2xiaomai/ref/ann/9.SNP_Analysis/2.bam_process/CH.bam.split.bam --tmp-dir /share/nas1/renzx/project/zx-20210524-20_BSR_2xiaomai/ref/ann/9.SNP_Analysis/tmp --create-output-bam-index false

然后自己给bam文件创建索引。

samtools index -c CH.bam.split.bam

以上就是"SNP分析中报错怎么解决"这篇文章的所有内容，感谢各位的阅读！相信大家阅读完这篇文章都有很大的收获，小编每天都会为大家更新不同的知识，如果还想学习更多的知识，请关注行业资讯频道。