My question Is some how 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 this that also each sample have 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?