Haplotyping/genotyping tool PacBio?

[BioGenomics]

Hi all,

we have data from 40 different amplicons of different sizes (400 - 4000 bp) that have various coverage levels sequenced in a plant, hence LAA struggles with this dataset (clustering approach not optimal and uneven coverage main issues). Ultimately, I'd like to have a set of haplotypes/genotypes (polyploid plant) per individual, where I can simply estimate allele frequencies in a population later and to report variants. We tried Freebayes as well, but it splits the full amplicons into linked chunks, while source data (amplicon length) is what we need.

Hence, does anybody know a good tool to cluster/align CCS reads into amplicon specific haplotypes/genotypes as alternative to LAA ?

thanks !

[rhall]

Are all the amplicons from distinct regions, or are they overlapping?
The first thing I would try is to run LAA, but only on a single amplicon at a time, that way the coarse clustering is redundant, but the phasing should work. Start by aligning the amplicons to the reference, then for each location generate a list of the reads that map within it. This list can then be used as a whitelist https://github.com/PacificBioscience...tasetWhitelist to run LAA independently for each amplicon.

[BioGenomics]

thanks rhall,

indeed, running LAA per amplicon was an idea we had as well, the whitelist will then increase analysis speed ! We'll give it a go soon.

If any other tool available for the the non-model community, just shoot some suggestions !

to be continued...