出现这种问题说明bam/cram文件没有进行index.
Samtool能解决这个问题,以bam文件为例,输入以下命令行即可解决问题:
/path/to/your/samtools index file.bam
外显子分析弹错解决方案:Invalid command line: Cannot process the provided BAM/CRAM file(s) because they were not indexed.
原文:http://www.cnblogs.com/chenwenyan/p/7747568.html