I am new to long read seq, I am trying to call Variants on GIAB Trio samples from PacBio data
Initially i Aligned reads with Pbmm2 tool, then variant call by DeepVariant 1.5, Phasing through Whatshap.
My queries are as follows Like Illumina NextSeq/NovaSeq data
What are Quality parameters that should be taken care ( Adapter trim, Reads filter, Min Data size, ) How to trim adapter, What tools to use for FastQ/BAM input from PacBio for QC.
I have Phased data after Whatshap which are represented
"|" in VCF, Does that mean should i filter out the variants that has
"\" before downstrean analysis annotation ( Are they bad quality variants )