Hi, I'm looking for some tools to perform SNP calling on some of BAM alignment data. The data on which I am doing research come from Illumina technology (average coverage 300x) and PacBio (average coverage 30x). Does anyone know give me some suggestions on which are the best tools in the literature?
As far as I can see, no common variant callers work on Pacbio Sequel data (bacterial, read length ~3-5 kbp, coverage 200-300x).
Supporting VCF4 is essential for the Pacbio software SMRT analysis. I currently have two Pacbio projects for resequencing (and also methylation detection). The resequencing part of the more recent SMRT Analysis tools only generates VCF 3.3 from memory. VCF 4.0 (at least) however is essential to work with downstream VCF analysis tools such as Snpeff, vt etc.
Current leading variant callers such as Freebayes do not work on Pacbio BAMs (I believe the MD tags were too long). I need to try Samtools next, but at the moment cannot recommend Pacbio for resequencing.
It would be great if anyone has any solutions to this issue. Even if the callers perform less than optimally it would be good to find one suitable.