Visualizing pacbio-derived alignment in IGV

Question

[cugopal]

I have an alignment file (BAM) and an associated index file (pbi) delivered to me by the sequencing provider. I am trying to visualize the alignments in IGV (v2.8.0). I first tried to index the (sorted) BAM file using samtools as follows but it creates an empty index (bai) file.

samtools index alignment.bam

The resulting index file is essentially empty (16 bytes). Probably as a result, I don't see any information in the alignment track in IGV. (The FASTA file index, created with samtools faidx is fine).

IGV doesn't show anything when I indicate that the pbi file contains the index either.

How can I visualize the alignments?

[ATpoint]

That is the standard way of doing it. Is the BAM file ok? Are there mapped reads? Any error messages? Is the BAM sorted by coordinate?

[GenoMax]

PacBio BAM files can be of different types. Have you tried to see if the pbi index works? It seems to be an extension of usual .bai spec and IGV may understand it natively. Found a video here that shows IGV being used to visualize Sequel data.

[cugopal]

@ATpoint @genomax Yes, the BAM file only contains the reads, and not the alignment, which is what I assumed. Sorry. Thanks for your answers.

[GenoMax]

No problem. Be sure to use bam2fastx tool from PacBio to convert your files to fastq reads.

[cugopal]

Thanks for the pointer to bam2fastx. Does it produce a different result from e.g. samtools fastq?

[GenoMax]

If your BAM files has PacBio specific extensions that are referred to in the link above they may be lost by using plain samtools fastq.