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 more
Caused 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
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