Mapping using PacBio CCS BAM file

[gevro]

Hi, Is there any way to do this? This would be simpler than converting PacBio BAM files to fastq, and then somehow integrating the info from the original PacBio BAM file with the mapped BAM file.

Any other advice on best practices for aligning PacBio CCS data?
Thanks.

[cjain7]

PacBio BAM files are not supported as input currently. That said, do you know any long read mapper that does it? I could consider incorporating this feature if this is being done by any mapper.

Re: best practices for aligning PacBio CCS data
I think README file and winnowmap -h would give you sufficient information. Just go for default values in my opinion.

[gevro]

pbmm2 (a port of minimap2) supports PacBio BAM files.
https://github.com/PacificBiosciences/pbmm2

[jelber2]

Maybe you could try bazam (https://github.com/ssadedin/bazam) to go from PacBio BAM files to stdin of winnowmap? According to the readme, you can also call bazam as a library.

[gevro]

Perhaps. PacBio BAM files however contain additional tags with info on each read, which are lost in the process of converting to fastq.