error when reading bam files

[Natalia Berges]

Hi, I have the following problem when trying to read bam files created in Partek:

1. I am using the IGV version 2.4.10 and Windows. 
   
2. I opened a bam file and tried to zoom in or look for a gene. Every time I try something the error: Error encountered querying alignments: htsjdk.samtools.util.RuntimeIOException: Invalid file header in BAM index 5EVlong.bai: +Á#ú pops up.  
   
3. I expected I could view my reads aligned to the genome.
   
4. What actually happened, I got the error message, no reads from my file were ever showed.

I'm not sure how to proceed and fix this error. Is there something wrong with the bam files?

Thank you for your help.

Best,

Natalia

[James Robinson]

The error indicates a problem with the BAM index file.   I suggest you create the index. 

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[Wayne Henderson]

Hello 

Did you manage to solve this issue?

Because I am facing the same problem. 

[igv-help]

If you are having the same issue,  the cause would be the same.   An invalid BAM index file.