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 tool 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 ...

deepconsensus 1.2 snakemake pipeline

This snakemake-based workflow takes in a subreads.bam and results in a deepconsensus.fastq

• no methylation calls !

The metadata id of the subreads file needs to be: "m[numeric][numeric][numeric].subreads.bam"

Chunking (how many subjobs) and ccs min quality filter can be adjusted in the config.yaml

the checkpoint model for deepconsensus1.2 should be accessible like this: gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* ...