Error loading a bam + bai files in IGV

0

Entering edit mode

2.2 years ago

jjeang • 0

Hello,

I have a bam and its corresponding bai file that I am trying to view in IGV. However when I try to load the files I get the following error message

Error querying alignments for: /path/mydata.bam Error message: /path/mydata.bam has invalid uncompressedLength: -208504753

I suppose this means the bam file was processed incorrectly somehow? Or is it that the bai file is funky and the length of the bam file is getting computed as something weird? Either way, I'm not sure what to do differently to fix this. Has anyone seen this error before, or have a hunch as to what's going on here?

I should note that I have gotten IGV to work in the past so I don't believe the problem is with my IGV application. But for completeness the IGV version is 2.13.2.

Thanks

IGV Bai Bam Alignment • 1.1k views

ADD COMMENT • link updated 2.2 years ago by young_bioinformatician ▴ 240 • written 2.2 years ago by jjeang • 0

0

Entering edit mode

They have already discussed the same error in github: invalid uncompressedLength

ADD REPLY • link 2.2 years ago by young_bioinformatician ▴ 240

Login before adding your answer.