Amplicon variant calling from PacBio CCS reads

Question

[vaslanzadeh]

Hi,

I sequenced a 3kb amplicon library generated by saturation mutagenesis with PacBio. Each amplicon has a unique barcode at the 5' end and a random mutation along the sequence. CCS reads were aligned to the reference gene with pbmm2. Now, I want to generate an output file that lists ZMW number (or read ID) and associated mutation(s). I spent several days to use SMRTlink tools to generate such output with no success. What would be the best way to generate this output?

Thanks

[GenoMax]

Do you have an alignment BAM to your reference? Can you not parse the BAM file which should have this information?

[vaslanzadeh]

I just discovered running "samtools calmd" with -e flag. The output is very close to what I expected. Now I want to see if the output includes all the SNPs, indels and deletions. Next step would be parsing this output and generating a file with two columns, read name and variant.