how to generate bam.pbi (PacBio BAM index)? about pbcore

[dbrowneup]

I've found that if you are using a pitchfork deployment of BLASR/GenomicConsensus, that there is a tool available called pbindex that will generate the .pbi

Usage: pbindex <input>

pbindex creates a index file that enables random-access to PacBio-specific data
in BAM files. Generated index filename will be the same as input BAM plus .pbi suffix.

Options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

  Input/Output:
    input               Input BAM file

[dalexander]

Hi, there is a tool "makePbi.py" provided in GenomicConsensus

[peterjc]

While otherwise quite comprehensive, https://pacbiofileformats.readthedocs.io/en/5.1/PacBioBamIndex.html does not describe how to generate a *.bam.pbi file from *.bam

Note also that pdindex can be installed with conda install pbbam, see
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pbbam/meta.yaml