best practices to use GATK with PacBio

Question

[Medhat]

My question Is somehow related to this previous post with some differences

Order Of Gatk Commands

I have 2 samples each contains 4 libraries and each library formed of 8 Illumina lanes,

add to that, each sample has PacBio library.

My question is,

How can I make use of PacBio reads:

• shall I treat the pacbio library like any other library except for the step of Realign Indels I shall skip it in the pacbio reads, but I shall do it for the rest of libraries normally!
• Or correct the pacbio reads with illumnia for example, then use only the corrected pacbio reads with GATK?

regarding if I will treat PacBio like just another library shal I use the corrected PacBio reads Or the subreads

any previous experience Or Idea?

Answer 1

[prasundutta87]

GATK has not been developed keeping long reads (such as PacBio) in mind. It should only be used for short reads (such as illumina). For variant calling from PacBio reads, its better to use their own variant caller- GenomicConsensus (https://github.com/PacificBiosciences/GenomicConsensus)

[Medhat]

The question was around 3 years ago, there are tools now available for LR. This is an example: https://github.com/aquaskyline/Clairvoyante .

Thanks for suggestion