News

ATAV 6.5.9

Added by Nick Ren about 1 month ago

Improvements:
  • Update KnownVar 2017 Q2 (issue #2345)
Changes:
  • Polyphen score for CCDS transcripts (issue #2362)

ATAV 6.5.8

Added by Nick Ren 2 months ago

New features:
  • Added new genotype QC filter command options that can be used separately for SNVs and indels. (issue #2338)

Ex. --snv-fs 60, --indel-fs 200
For more QC filter options, check Genotype Level Filter Options.

ATAV 6.5.7

Added by Nick Ren 3 months ago

New Features:
  • Added gnomAD Exome dataset and command options (issue #2284):
    --gnomad-exome-pop
    --gnomad-exome-maf
    --gnomad-exome-as-rf-snv
    --gnomad-exome-as-rf-indel
    --include-gnomad-exome
    
Changes:
  • All ExAC command options refer to use v0.3 dataset (ATAV 6.5.5 and ATAV 6.5.6 used gnomAD Exome dataset for the following command options):
    --exac-pop
    --exac-maf
    --min-exac-vqslod-snv
    --min-exac-vqslod-indel
    --include-exac
    
  • --include-all-external-data command option disabled, check here for the command options to include external dataset in your analysis.

Please note that IGM has contributed samples in gnomAD, you need to check before using gnomAD data or continue using ExAC data.

ATAV 6.5.6

Added by Nick Ren 3 months ago

Bugs fixed:
  • Fixed wrong genotype count issue and missing values (ExAC Sample Covered 10x, ExAC AB MEDIAN, ExAC GQ MEDIAN, ExAC AS RF) in ExAC v2. (issue #2213)
New Features:
  • Added new ExAC filter --min-exac-as-rf-snv and --min-exac-as-rf-indel. (issue #2213)

Suggested cutoffs are prob >= 0.1 (high-confidence SNVs) and prob >= 0.2 (high-confidence indels)

ATAV 6.5.5

Added by Nick Ren 4 months ago

Improvements:
  • Update ExAC from version 0.3 to 2.0 (issue #2213) - beta version

Added one more population: ASJ
Added four additional fields:

ExAC filter
ExAC AB MEDIAN
ExAC GQ MEDIAN
ExAC AS RF

--min-exac-vqslod-snv and --min-exac-vqslod-indel is no longer support since VQSLOD doesn't perform well at large scale joint-calling.

ATAV 6.5.4

Added by Nick Ren 4 months ago

Bugs fixed:
  • Invalid input genes caused ATAV crash (issue #2079)
New Features:
  • Kinship relatedness pruning (--kinship) integrated in --ped-map function (issue #2148)
  • Add new external dataset DenovoDB (issue #2149)

using --include-denovo-db to include denovo-db variants in the final output when ran a variant based functions.
using List Denovo DB to output variant denovo-db variants only.

Improvements:
  • Update KnownVar 2017 Q1 (issue #2164)

Upgraded dataset: HGMD, ClinVar, ClinGen, OMIM, MGI

  • Update trio run tier data filtering process (issue #2156)
  • Output pruned sample file when run --ped-map function with --eigenstrat option (issue #1960)

ATAV 6.5.3

Added by Nick Ren 7 months ago

Bugs fixed:
  • Job crash when generating permutation QQ plot (issue #2035)

ATAV 6.5.1

Added by Nick Ren 7 months ago

Bugs fixed:
  • --site-coverage-comparison output wrong aggregated info in the log file. (issue #2007)
New Features:
  • Inclusion of Binomial Exact Test in Collapsing Analysis Output & Filter. (issue #2014, #2015)
Improvements:
  • KnownVar dataset upgraded: ClinVar, HGMD, ACMG, OMIM. (issue #1951)
  • Multiple Frequency Bands for --het-percent-alt-read. (issue #1884)
Changes:
  • Flag deletions supported by inherited genotypes in trio rules. (issue #1988)
  • chip2pca replacement. (issue #1960)

ATAV 6.5

Added by Nick Ren 9 months ago

Bugs fixed:
  • permutation based empirical QQ plot for collapsing analysis (issue #1161)
  • eigenstrat changes output ped files to Indicating all samples are Unaffected (issue #1636)
New features:
  • add dbDSM as part of KnownVar output (issue #1872)

a manually curated database for deleterious synonymous mutations

  • add new trio comp het flag "denovo with inherited variant" (issue #1776)
Changes:
  • list trio denovo and list trio comp het combined into one function: --list-trio (issue #1776)

--list-trio-denovo and --list-trio-comp-het is no longer support

  • added --rs-number option (issue #1821)

--variant option is no longer support rs number as input values

  • --min-trap-score filter applied only when variant's most damaging effect type is SYNONYMOUS_CODING or INTRON_EXON_BOUNDARY or INTRONIC (issue #1694)
Improvements:
  • knownvar data update (issue #1808)
  • include transcript ID and CCDS trnascript status (issue #1855)
  • support --region option in some external dataset functions (issue #1817)
  • standarize external data version (issue #1806)

ATAV 6.4.2

Added by Nick Ren 11 months ago

New features:
  • Add a new sub option --run-tier in --list-var-geno function (issue #1768)

trigger to run non-trio tier script at the end.

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