Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
With an input CRAM file pindel expects the index to have an extension .cram.bai which is incorrect as CRAM files indexes have the extension .crai .
CRAM files that are correctly indexed generate the error 'I cannot find the bam index-file'.