Loading BAM and BAI files

[sc...@ncsu.edu]

Hello,

1. I have SAM file.

2. I converted sam file to bam file.

3. The bam file was sorted.

4. The sorted bam file was indexed.

5. Finally, sorted bam and bai file were gained.

6. When I tried loading bam and bai files, ERROR message keeps occurring:

  - ERROR: Loading SAM/BAM index files are not supported. Load the SAM or BAM file directly.

  - Could not load index file. An index file is required for SAM and BAM files.

7. Would you please help me to fix these errors?

Thanks in advance.

[sc...@ncsu.edu]

P.S. I am running IGV2.3 on windows.

[Jacob Silterra]

Hello,

When you use File -> Load to select a file, select the .bam file, and not the .bam.bai index file.

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute

[Site on]

Hi,

Of course I did.

When I tried loading BAM file, an error message said, "Could not load index file. An index file is required for SAM and BAM files."

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[Jacob Silterra]

Hello,

Can you send your igv.log file? It should be in <home directory>/igv/igv.log

Thanks,

-Jacob

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[Soyeon Cha]

Hello,

Would you please see the attached file and give me a piece of advice?

Thank you so much!

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[Jacob Silterra]

Hello,

It looks like there is an index for the unsorted BAM file, but not the sorted BAM file. So create an index for chwd3_abyss-map_sorted.bam and you should be all set.

-Jacob

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[sc...@ncsu.edu]

Hi,

The "bai" file is the one which was generated from the sorted "bam" file.

So when I just changed the file name from "chwd3_abyss-map.bai" to "chwd3_abyss-map_sorted.bai", it worked very well.

Thank you very much for prompt reply and your advice!!!

[Cara Fiore]

Hello,

I have the same question as on this post - however, the answer here does not fix my problem. 

I have the bam file, the sorted bam file, and the indexed bam file all in the same directory and when I try to load the bam file I get

"Could not load index file. An index file is required for SAM and BAM files."

My files are named:

ALLtrinity.bam

ALLtrinity.sorted.bam

ALLtrinity.sorted.bam.bai

I also tried changing the .bai file name to remove the ".bam" but that did not help. 

I also tried using the sam file and indexing it with IGVtools but that gave me a file error too and would not work.

Any help is greatly appreciated.

Cara

[Jim Robinson]

Hi,

Dumb question,  but I assume you are loading ALLtrinity.sorted.bam, as opposed to ALLtrinity.bam.   Could you confirm?  

I'll need your igv.log file to help further.

Jim

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[Cara Fiore]

Hi Jim,

Thanks for the quick response. So I am not sure if this was my error or just needing to reboot the program because I actually tried all three files before this just in case. Now I just tried again after closing down the program and yes loading the sorted file works! I apologize for my confusion on this I had just been trying so many things! Thank you for your time!

Cara

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[touta....@gmail.com]

Hi, I am having a problem here, can you help me please, I am getting this msg and I am unable to view my sequence

Error loading C:\Users\TOSHIBA\Desktop\Diabetes stuff\PAHRMACOGENOMICS_BAASAM_10_11_19\A1_R_2~1.BAM: An error occurred while accessing: C:\Users\TOSHIBA\Desktop\Diabetes stuff\PAHRMACOGENOMICS_BAASAM_10_11_19\A1_R_2~1.BAM

Error loading BAM file: org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: C:\Users\TOSHIBA\Desktop\Diabetes stuff\PAHRMACOGENOMICS_BAASAM_10_11_19\A1_R_2~1.BAM.bai
Index file not found. Tried
C:\Users\TOSHIBA\Desktop\Diabetes stuff\PAHRMACOGENOMICS_BAASAM_10_11_19\A1_R

[James Robinson]

Does this file exist?   C:\Users\TOSHIBA\Desktop\Diabetes stuff\PAHRMACOGENOMICS_BAASAM_10_11_19\A1_R_2~1.BAM.bai