> INFO 15:19:52,909 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 15:19:52,908 HelpFormatter - The Genome Analysis Toolkit (GATK) ![]() > -md wild_rice_test2/metadata -createEmpty > /home/wbxie/software/svtoolkit/installtest/wild_rice_test2/metadata/isd/ > /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I > /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar > -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir However, When I came to more BAM files, some of the ![]() If this doesn't fix the problem, I would try "samtools view" to see if I would try reindexing the file with "samtools index C046.bam" It is likely that your bam file or bam index file is corrupted.
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