Samtools error - Fail to load BAM index when using samtools view

Question

[alvastrand]

Hi,

I am trying to split my bam file into individual files containing data for each chromosome, and I know how to do that. The problem is that when I write:

samtools view myfile.bam 1

(for example, to just view the data for chromosome 1)

I get the following error message:

[bam_index_load] fail to load BAM index. 
[main_samview] random alignment retrieval only works for indexed BAM files.

The strange thing is that I already have indexed myfile.bam, so I don't understand why it would fail to load the index if it's there, ready to use.

If anyone could help, that would be great.

Thanks,
Alva

[Ram]

Maybe the index file does not follow the expected naming. What is the name of the index file? It should be myfile.bai

[komal.rathi]

It shouldn't fail if you have a myfile.bam.bai in the same folder. Other than that, if you want to view data from chr1,

samtools view myfile.bam chr1

[alvastrand]

Someone else had indexed the bam file using another method; when I copied the file and usedsamtools index myfile.bam, it worked. Thanks for the help, both here and below.

Answer 1

[Pierre Lindenbaum]

your BAM file was not indexed.

Run

samtools index your.bam

[chandrugenetics]

Thanks Mr.Pierre, It worked.