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DeepVariant 1.0.0
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@pichuan pichuan released this 03 Sep 17:45
· 12 commits to r1.0 since this release
v1.0.0
7ed651e

DeepVariant v1.0 releases new features and accuracy improvements sufficiently substantial to indicate a major version of v1.0. Compared to DeepVariant v0.10, these changes reduce Illumina WGS errors by 24%, exome errors by 19%, and PacBio errors by 52%.

  • Added ALT-aligned pileups, which creates additional input channels where reads are also aligned to the candidate ALT alleles. This is controlled by the flag --alt_aligned_pileup. --alt_aligned_pileup=diff_channels is now default for DeepVariant PacBio model. This substantially improves INDEL accuracy for PacBio data.
  • Added new flag --sort_by_haplotypes to optionally allow creating pileup images with reads sorted by haplotype. Haplotype sorting is based on the HP tag that must be present in input BAM, and --parse_sam_aux_fields needs to be set as well. This substantially improves INDEL accuracy for PacBio data.
  • The PacBio case study now includes instructions for two-pass calling, which allows users to take advantage of the --sort_by_haplotypes by phasing variants and the input reads. Accuracy metrics for both single pass calling and two-pass calling are shown. Users may choose whether to run a second time for higher accuracy.
  • Default of --min_mapping_quality in make_examples.py changed from 10 to 5. This improves accuracy of all models (WGS, WES, and PACBIO).
  • Included a new hybrid illumina+pacbio model and documentation.
  • Added show_examples, a tool for showing examples as pileup image files, with documentation.
  • Cleaned up unused experimental flags: --sequencing_type_image and --custom_pileup_image
  • Added --only_keep_pass flag to postprocess_variants.py to optionally only keep PASS calls in output VCF.
  • Addressed GitHub issues:
    • Fixed the binarize function in modelling.py. (#286 fixed in db87d77)
    • Fixed quoting issues for --regions when using run_deepvariant.py. (#305 fixed in fbacd35)
    • Added --version to run_deepvariant.py. (#332 fixed in f101492)
    • Added --sample_name flag to postprocess_variant.py and applied it in run_deepvariant.py as well. (#334 fixed in a81d629)
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