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ATAV 7.4
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@nickzren nickzren released this 22 Mar 20:04
· 17 commits to master since this release
7.4
6917cdd

Bug fixed:

  • Fixed OMIM data parsing issue when alternative gene names are the identical for two different genes. (issue #8573)

New Feature:

  • More stringent to diagnostic flag output (issue #8502)

    • Single Variant Prioritization and (Tier 1 or 2 or LOF or KV or ATAV classified as P/LP)
    • Default exclude synonymous and splice region variants from flag output unless TraP score >= 0.4
    • LoF variant only determined by variant's effect (ignore to check TraP score)
    • Changes to tier 2 inclusion criteria: a) changed 2pb flanking P/LP to site P/LP; b) removed two missense variants rules
    • More stringent to KV and LOF Gene flagged variants

  • Added new sub option --phenolyzer-ph to --list-singleton and --list-trio (issue #8111)

    • this option allow to input HPO terms and trigger ATAV to run phenolyzer then output phenolyzer rank and score to final output.

  • Added new gene level function --list-gene-anno (issue #8386)

    • this function allow input gene list and output all gene level annotations from ATAV

  • KnownVar data updated. (issue #8575)

    • HGMD: 2022.4
    • ClinVar: 2023-03-20
    • ClinVarPathoratio: 2023-03-20
    • MGI: 2023-03-20
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