pb_variants

A snakemake 9 based Pipeline for hifi snp, sv, cnv calling, phasing and more

Only PacBio data for now

!!THIS PIPLINE IS IN-DEVELOPMENT AND EXPERIMENTAL, USE AT YOUR OWN RISK!!

what this tools aims to deliver:

• newest and best tools suited for HiFi data (only for now)
• singletons and trio analysis (trio is coming sometime...)
• human-first (hg38 for now), others should be possible (untested...)

included tools:

• deepvariant or bcftools for snp calling
• snps get used for ...

GermlineStructuralV-nf is a pipeline for identifying structural variant events in human Illumina short read whole genome sequence data. GermlineStructuralV-nf identifies structural variant and copy number events from BAM files using Manta, Smoove, and TIDDIT. Variants are then merged using SURVIVOR, ...

StructuralVariants Workflow

StructuralVariants Workflow