samtools tview

[EmmaB]

I am having a problem with the tview option in samtools.

I am using this command
samtools tview 5673_5_t8.sortedbam.bam ./genomes/NC_013316.fna

but keep getting this error -
[bam_index_load] fail to load BAM index.

I have previously used this exact command to view the file correctly, but now it wont work!!

Is anyone else having similar problems? I have tried to index the sorted bam file, but this doesn't help either.

Has anyone any suggestions?

Cheers

Emma

[SOLiDance]

Maybe you should try re-index the bam file with the same ref? For example: samtools faidx ref.fasta, then use the .fai to get the sorted bam?
I'm just a beginner,not sure about it~ Hope can help

[EmmaB]

tview

Hi,

Thanks for your post. I tried indexing the BAM file and it didn't work.
The problem seems to be temperamental, I just retyped my original command and tview worked, then I quit the programme retyped the exact same command and it did not work!

very puzzling!

[fpepin]

samtools is complaining about not finding an index file in the same directory: 5673_5_t8.sortedbam.bam.bai. Is one there?

If not, then you want to create one using:
samtools index 5673_5_t8.sortedbam.bam

I'm not sure why tview would succeed/fail on the same command, but hopefully the problem will be fixed if you create the index.

[EmmaB]

tview

Thanks for the replies.
I started again from the original BAM files, sorted and indexed them.
All seems to be fine now, so I think I must have been mistyping something!

Oh to be a Unix newbie (NOT)!

Cheer

Emma