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Today, I would like to share with you the relevant knowledge points about how to solve errors in SNP analysis. The content is detailed and the logic is clear. I believe most people still know too much about this knowledge, so share this article for your reference. I hope you can get something after reading this article. Let's take a look.

In the process of SNP analysis, the length of the genome sequence is too long, which will cause the GATK software to report an error. It is as follows:

Exception in thread "main" htsjdk.samtools.SAMException: Exception when processing alignment for BAM index A00253:355:H75GLDSX2:2:1334:20989:8625 1 aligned read 2 150b. 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 1amp 2150b 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

You can add the-- create-output-bam-index false option at run time to prevent it from creating an index file for the bam file.

/ 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

Then create your own index for the bam file.

Samtools index-c CH.bam.split.bam above is all the contents of this article entitled "how to solve errors in SNP Analysis". Thank you for reading! I believe you will gain a lot after reading this article. The editor will update different knowledge for you every day. If you want to learn more knowledge, please pay attention to the industry information channel.

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