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PEPPER-Margin-DeepVariant release
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@kishwarshafin kishwarshafin released this 05 Mar 16:16
· 5 commits to r0.4 since this release
v0.4
464f615

This is the official release of PEPPER-Margin-DeepVariant. It supports the Nanopore and PacBio HiFi variant calling and assembly polishing pipelines.

Key highlights and improvements:

  • Candidate finding with PEPPER HP is implemented in a manner that is best suited for DeepVariant's image generation. You will not see any called variant with allele frequency 0 as the candidate finding is now synonymous with DeepVariant's candidate finding with RNN predictions used to rank the candidates. PEPPER-DeepVariant can be used as a standard small variant calling tool.
  • PEPPER SNP is improved and tuned to work with Margin in a manner that PEPPER-Margin produces the best haplotyping results for Oxford nanopore and PacBio HiFi data.
  • Overall we see a 30x improvement in the total runtime of the pipeline and PEPPER itself is 20x faster compared to r0.1. We are expecting more runtime improvements in the future.

Discontinued features:

  • PEPPER is not supported as a standalone assembly polishing tool. We believe the PEPPER-Margin-DeepVariant pipeline is much more sensitive to the structure of the assembly and provides a way to avoid over-polishing an assembly by filtering the VCF. This feature in itself is missing from PEPPER so we dropped haploid assembly polishing and overall assembly polishing with PEPPER alone.
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