ATAV 7.4.3

New Feature:

• KnownVar data updated. (issue #8685)
  • HGMD: 2023.2
  • ClinVar: 2023-07-10
  • ClinVarPathoratio: 2023-07-10
  • MGI: 2023-07-10

ATAV 7.4.2

New Feature:

• Added sample level filter --broad-phenotype (Ticket #8622)
• IGM AF data updated.
  • IGM AF: 2023-05-10

ATAV 7.4.1

New Feature:

• KnownVar data updated. (ticket #8610)
  • HGMD: 2023.1
  • ClinVar: 2023-04-17
  • ClinVarPathoratio: 2023-04-17

Improvement:

• Fixed ClinVar & HGMD site/flanking count performance issue. (ticket #8609)

ATAV 7.4

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

ATAV 7.3.3

Bug fixed:

• DP Bin parsing issue on borderline - #8204
• Check covered sample (include QC failed carriers) - #8194

New Feature:

• Add --site-max-percent-cov-difference as cohort level filter - #8021
• KnownVar update - #8105
• IGM AF update - #8118
• --gzip for list-var-geno-lite & collapsing-lite output - #8122

ATAV 7.3.2

New Feature:

• Add new filter --exclude-ttn-low-psi-lof-var. (issue #7804)
  ** use this filter to exclude LoF variants from TTN gene with PSI score < 90
  ** it applied by default when run diagnostic function
• KnownVar data updated. (issue #7859)

HGMD: 2022.2
ClinVar: 2022_07_18
ClinVarPathoratio: 2022_07_18
MGI: 2022_07_18

• IGM AF data updated.

IGM AF: 2022-07-15

ATAV 7.3.1

New Feature:

• ACMG Gene upgraded to v3.1. (issue #7816)

ATAV 7.3

New Feature:

• Add Variant Prioritization Flag to diagnostic analysis output for Variant reviewing SOP. (issue #7399)
  Add ATAV ACMG Classification to diagnostic analysis output. (issue #7367)
• KnownVar data updated. (issue #6928)

HGMD: 2022.1
ClinVar: 2022_04_08
ClinVarPathoratio: 2022_04_08
MGI: 2022_04_08

• IGM AF data updated.

IGM AF: 2022-04-22

Changes:

• DP Bin has been changed to either 10 or NA in the output.

ATAV 7.2.1

New Feature:

• KnownVar data updated. (issue #6928)

HGMD: 2021.4
ClinVar: 2022_01_10
ClinVarPathoratio: 2022_01_10
MGI: 2022_01_10

• IGM AF data updated.

IGM AF: 2022-01-03

Bug fixed:

• Collapsing light genotypes file parsing error. (issue #7275)

ATAV 7.2

New Feature:

• Add variant prioritization / tier classification and standard variant filtration workflow for diagnostic analysis (to --list-trio and --list-singleton). (issue #6956)
• Add a new diagnostic function called --list-singleton. (issue #7020)
  ** it supports tier classification rules by default
• Add IGM Default Control AF (10k samples) to output and to filter variants. (issue #6870)
• KnownVar data updated. (issue #6928)

Changes:

• Output de novo, homozygous/hemizygous, inherited and compond heterozygous variants to a single output (flagged and non flagged). (issue #6928)
• Changes to output HGMD DM and ClinVar PLP flanking region count. (issue #6975)
• Treat ClinVar 'Conflicting_interpretations_of_pathogenicity' variant same as P/LP if CLNSIGCONF only contains P/LP or VUS. (issue #7047)