PacBio Pipeline and Tools for Variant Call

PacBio Pipeline and Tools for Variant Call

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Hi,

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 )


longread


pacbio


whatshap


pbmm2

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