 06/06/2024 |
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Fix a bug in output of ANNOVA format.
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| 04/29/2023 |
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Fix a bug in resource data location of dbNCFP scores.
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| 04/11/2023 |
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Allow KGGSeq to read a highly addressable byte-encoding genotype blocking format, GTB.
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| 01/30/2023 |
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Fixed a minor bug for annotating variants in duplicated genomic regions.
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| 09/27/2022 |
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Fixed a bug in the new algorithm (released on 08/26/2022) of variants' gene feature annotation for Indels.
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| 08/26/2022 |
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Improve the speed of variants' gene feature annotation.
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| 07/26/2022 |
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Add clinvar_clnsig and clinvar_trait of dbNSFP4.2a into the output file.
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| 01/01/2022 |
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1. Update resources of KGGSeq, including RefGene, GEncode, UCSC gene models and dbNSFP4.2a.
2. Add variant expression in multiple tissues and cell-types from GTEx.
3. Add more analysis options for RUNNER.
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| 11/16/2021 |
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1. Allow RUNNER to consider customized weights of variants.
2. Add mutation rates of gnomAD as covariates of RUNNER.
3. Enable uses to select C/T types variants for all analysis.
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| 09/25/2021 |
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1. Adjust the disease statues (--phen) by covariables (--cov) with the logistic regression (--adj-disease) for RUNNER.
2. Allow to exclude genes with only one variant (--ignore-gene-fewer-var 1).
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| 02/18/2021 |
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Fixe kggseq's resource download-link for the new website.
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| 07/17/2020 |
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Fixe a resource bug for RUNNER analysis based on reference genome hg38.
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| 06/16/2020 |
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Simplify options for mutation burden tests by setting default parameters.
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| 03/18/2020 |
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Upgrade KGGSeq from v1.1 to v1.2 in which a new analysis named Pheno-RUNNER is integrated.
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| 03/01/2020 |
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Update the gnomAD genome R3.0 for hg38.
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| 12/07/2019 |
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Fix a bug for option '--genes-out'.
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| 11/28/2019 |
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Fix a minor bug in checking R packages.
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| 11/20/2019 |
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Fix a minor bug in double-hit filtering.
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| 10/30/2019 |
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Fix a minor bug in searching allele-frequency of indels.
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| 10/03/2019 |
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Fix a minor bug in output of RVTESTS analysis.
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| 08/19/2019 |
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Improve the input and output of RVTESTS for gene-based association.
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| 07/06/2019 |
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1. Add a new analysis function, WITER, into KGGSeq for estimating cancer-driver genes. See details in the user manual.
2. Fix a bug of missing unlabeled variants in gene feature filtering.
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| 03/29/2019 |
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1. Add a new analysis function, RUNER, into KGGSeq for a powerful genetic mapping of rare susceptibility mutations in patient-only and case-control samples. See details in the user manual.
2. Fix a bug of missing unlabeled variants in gene feature filtering.
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| 03/05/2019 |
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Fix a minor bug for merging downloaded dbncfp files.
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| 02/18/2019 |
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Fix a minor bug for using dbnsfp and dbncfp together in --db-score.
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| 01/15/2019 |
Update the v1.0 to v1.1. In which there are 2 major updates besides fixing some minor bugs.
1. The program coding structure is revised substantially.
2. Update refGene model and gnomAD dataset to be v2.1
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| 11/17/2018 |
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Fix a minor bug in regulatory prediction at non-coding variants.
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| 6/20/2018 |
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Fix a minor bug in numbering the affected exon in gene feature annotation.
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| 4/10/2018 |
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Fix a minor bug in filtering variants by allele-frequencies for InDels.
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| 3/16/2018 |
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Fix a minor bug in predicting pathogenic mutations for Mendelian diseases.
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| 1/25/2018 |
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Fix a minor bug in predicting regulatory potential by some cell types.
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| 1/12/2018 |
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Fix a minor bug in allele frequency annotation for InDels of multiple alleles.
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| 1/8/2018 |
1. Annotate genes with tissue- or cell-type specific expression.
2. Improve prediction model for cancer driver mutations.
3. Update the variant annotation with dbSNFP v3.5
4. Update OMIM information.
5. Update Cosmic database to be V83.
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| 9/11/2017 |
Fix a minor bug of counting variants in genes
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| 7/20/2017 |
Fix a minor bug of missing indel variants in output VCF files.
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| 7/10/2017 |
Fix a minor annotation bug for variants with mixed substitution and insertion.
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| 6/30/2017 |
Fix a minor annotation bug for frameshift and non-frameshift variants
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| 5/18/2017 |
Allows KGGSeq to jointly annoate non-synonymous variants and splicing variants within X bp for each subject when phased genotypes in VCF format are available. See more.
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| 5/4/2017 |
Fix a minor bug in allele frequency annotation by dbNCFP.
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| 4/14/2017 |
1. Fix a minor bug in allele frequency annotation by exac.
2. Add allele-frequencies from Genome Aggregation Database (gnomAD),which contains 123,136 exome sequences and 15,496 whole-genome sequences from unrelated individuals |
| 3/28/2017 |
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Fix a minor bug in the function of gene feature annotation at deletion variants. |
| 3/28/2017 |
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Updated the ExAC database from v0.3 to v1.0 and fixed a bug of unmatched alleles at deletion variants. |
3/26/2017 |
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Fix a bug in LD pruning! |
| 3/18/2017 |
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Add a function tissue or cell-type specific epigenomic weighting for prioritization of regulatory variants and disease-associated gene. |
| 3/8/2017 |
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Allow KGGSeq to accept a super simple VCF format which only contains the first 5 columns(#CHROM POS ID REF ALT). |
| 2/25/2017 |
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Update the download link of mouse phenotype dataset. |
| 2/10/2017 |
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Fix a bug in pathogenic prediction under the feature specific model. |
| 1/28/2017 |
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Fix a bug of missing annotation by dbNSPF dataset. |
| 1/26/2017 |
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Add non-synonymous allele frequencies from DiscovEHR Collaboration, which contains over 50,000 paticipants. |
| 12/29/2016 |
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Fix a bug in parallel computing with the R package 'snow'. |
| 12/16/2016 |
1. Fix a bug in a VCF with a mixture of phased and unphased genotypes.
2. Update the protein interaction database STRING to be V10.
3. Update the gene set database GSEA to be V5.2. |
| 12/10/2016 |
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Fix a bug in knockout mouse annoation. |
| 11/25/2016 |
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Update the variant and frequency information of ExAC database (to r0.3.1) in which 60,706 unrelated individuals sequenced. |
| 11/14/2016 |
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Fix a bug for frequency-based filter for deletions. |
| 11/08/2016 |
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Fix broken conection to NCBI PubMed. |
| 11/02/2016 |
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Change the prediction model for pathogenic variants of mendelian diseases. |
| 10/28/2016 |
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Fix a bug in computing regulatory composite scores.
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| 10/18/2016 |
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Count double-hit genes in unaffected offspring of a trio.
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| 10/16/2016 |
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Fixed a bug in producing index file for RVTESTS.
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| 9/24/2016 |
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Fixed a minor bug for RSID annotation with hg38.
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| 9/18/2016 |
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Fixed some minor bugs for hg38.
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| 8/24/2016 |
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Fixed the broken link for DDD dataset.
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| 7/28/2016 |
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Add a tag for a VCF file containing both uphased and phased genotypes.
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| 7/21/2016 |
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Fix a minor bug in IBS estimation
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| 7/14/2016 |
1)Reduce the size of output genotype data in KED binary format.
2)Fix a minor bug in building index file.
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| 7/7/2016 |
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Fix a minor bug in the unique gene filter (--unique-gene-filter).
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| 6/28/2016 |
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Fix a minor bug in output format.
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| 6/21/2016 |
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1. Update the function for functional or regulatory prediction at whole genome variants .
2. Update the function for pathogenic prediction at genes.
3. Fixed a bug for annotation by known genes at for zebrafish and mouse .
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| 5/9/2016 |
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Fixed a bug in COSMIC cancer annotation.
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| 5/5/2016 |
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Fixed an output bug of reads for de novo mutations.
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| 04/27/2016 |
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Fixed a minor bug in annotation of dbNSFP dataset.
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| 04/24/2016 |
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Speed up the filtering by allele frequencies by a multiple-thread matching function.
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| 04/18/2016 |
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Add a function of LD pruning.
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| 04/12/2016 |
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Fixed a minor bug in resource downloading.
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| 04/02/2016 |
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Fixed the modified URL and format in the Development Disorder Genotype – Phenotype Database.
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| 03/30/2016 |
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Fix a minor bug in QQPlot of RVTESTS.
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| 03/10/2016 |
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Refine detailed gene feature annotation labels for InDels.
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| 03/06/2016 |
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Fixed some minor bugs in parsing annoation data with the faster algorithm.
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| 02/26/2016 |
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Improve the speed of parsing compressed annotation.
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| 02/02/2016 |
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Improve the function of VCF parsing to tolerate some ill-formats.
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| 01/05/2016 |
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Improve the association analysis with RVTest, in which the analysis models be can flexibly specified via KGGSeq.
|
| 12/28/2015 |
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Fixed a minor bug for Hardy-Weinberg test.
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| 12/24/2015 |
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Fixed bugs in producing input files for plink and RVTest.
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| 12/20/2015 |
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Optimize memory usage for large scale input.
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| 12/12/2015 |
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Release KGGSeq V1.0, which has a milestone upgrade for large-scale whole genome sequencing studies of complex diseases. See more in the online user-manual..
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| 10/28/2015 |
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Fixed a bug in gene-feature annotation for non-synonymous variants.
|
| 4/23/2015 |
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Fixed a bug in IBD region filtering.
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| 3/25/2015 |
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Format the output of gene feature annotations as Human Genome Variation Society(HGVS) recommendations.
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| 3/20/2015 |
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Refine the gene feature annotation. Add the stop-loss gene feature annotation for variants.
|
| 2/28/2015 |
1. Update dbNSFP to be version 2.9.
2. Fix a bug for the option --genes-in.
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| 1/18/2015 |
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Restructure the resource data folders of kggseq.
|
| 12/18/2014 |
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Update the function of gene-based analysis for cancer driver mutations.
|
| 12/2/2014 |
1. Update dbNSFP to be V2.8.
2. Fixed a minor bug for --double-hit-gene-trio-filter.
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| 11/24/2014 |
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Add variants in the exac dataset for filtration
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| 11/21/2014 |
1. Improved the basic gene future annotation with RefGene database (more accurate).
2. Fixed a bug to export ANNOVAR format for Deletion variants.
|
| 11/18/2014 |
1. Add gene feature annotation from Ensembl database.
2. Optimize the VCF parsing algorithm for using less memory.
|
| 9/11/2014 |
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Fixed potential Exception bugs in parsing VCF and sorting variants!.
|
| 25/10/2014 |
1. Add the latest version of 1000 Genomes Project data for data merging ;
2. Optimize the function of merging 1000 Genomes data.
|
| 22/10/2014 |
1. Refine filtering by reference variants. See more.
2. Provide a dataset dbsnp138nf for hard filtering without consideration of allele frequencies. |
| 10/07/2014 |
1. Add an option '--no-qc' to turn off all quality control function at variants and genotypes in VCF format.Thank Ricky Lali for the suggestion!
2. Add "--missing-gty X" to denote missing genotypes in the output VCF file. It is "--missing-gty ./." by default. For vcf-tools, one should set "--missing-gty .". Thank Lorenzo Tattini for the suggestion!
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| 10/03/2014 |
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Fixed two minor bugs, 1)getting stuck and 2)missing genotypes for vcf output. Thank Mike Chong for reporting the bugs!
|
| 09/29/2014 |
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Fixed a bug to parse numeric values from text.
|
| 09/24/2014 |
1. Fixed typos in the log file.
2. Further optimize the text search engine to speed up the procedure.
|
| 09/18/2014 |
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Integrate the functional prediction scores in dbNSFP 2.7 to predict pathogenic variants for Mendelian diseases and cancers! A new prediction score, VEST3_score, is added..
|
| 09/04/2014 |
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Optimize the prioritization and filtering procedure to speed up the analysis.
|
| 09/03/2014 |
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Integrate reference variants released by 1000 Genome Project in 2013 May (containing over 81 million sequence variants from 2504 subjects).
|
| 09/01/2014 |
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Fixed a minor bug in reference allele frequency-based filtering.
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08/27/2014 |
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Improve the output of LOG information and allow the screen LOG information redirect in a file.
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| 08/08/2014 |
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Allow VCF input without any phenotype information for basic annotation and prioritization.
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| 07/27/2014 |
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Correct errors about allele frequencies in dbSNP 137 and 138 and add dbSNP141 for allele-frequency-based filtering.
|
| 07/17/2014 |
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Fixed a minor bug for allele frequency filtering.
|
| 05/15/2014 |
Incorperate dbsnp138 for filtering and clarify variants with missing allele frequncies and not existing in databases. See more here .
|
| 05/03/2014 |
Allow the ANNOVAR format to have a head row and multiple columns for comments. See more here .
|
| 05/01/2014 |
Add a function for gene-based filtering. See more here .
|
| 04/28/2014 |
Fixed a minor bug in summary statistics of eliminated variants.
|
| 04/16/2014 |
1. Add two variant-filtering functions by super-duplicate regions and the number variants in a gene .
2. Save resulting variants in Excel2007+ format which have larger capacity than Excel1997.
|
| 04/10/2014 |
Fixed a bug in finding matched Indels. Thank JIBIN JOHN from UNIVERSITY OF DELHI for reporting the problem and preparing the testing data!
|
| 03/20/2014 |
Fixed small bugs for tri-allelic variants and exome length calculation.
|
| 03/14/2014 |
1. Update the pathogenic prediction models for Mendelian and cancer diseases with dbNSFP 2.4 .
2. Add more flexible functions for de novol mutation filtration.
|
| 02/15/2014 |
Add the UCSC known genes for variants annotation.
|
| 02/09/2014 |
Update dbNSFP to be version 2.3 in which there are less missing prediction scores.
|
| 01/24/2014 |
The gene set defined by GENCODE is used for gene feature annotation. An advantage of GENCODE over RefGene may be that the former contains genes definition mitochondria. here.
|
| 12/09/2013 |
Inproved the double-hit gene filtration function, See more in Double-hit gene filter.
|
| 11/21/2013 |
Incorporate genotypes from HapMap and 1K Genome Projects to more accurately check cross-subject contamination for small sample, See more in Sample QC.
|
| 11/9/2013 |
1. Update the deleteriousness prediction scores in dbNSFP to be version 2.1.
2. Fix several cryptic bugs. Thank Chong, Michael for reporting the bugs!
|
| 08/06/2013 |
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Fixed a bug for annoation of splicing variants. Thank Martin Haagmans for reporting the bug!
|
| 07/14/2013 |
1. Add a function to explore double-hit genes. See more here .
2. Refine an algorithm to speed up the exploration of longest IBS and homozygous genotype regions. See more here .
|
| 06/23/2013 |
1. Add two short tutorials for cancer-driver somatic mutation and de novo mutation analysis (see more by clicking the links on the upper-left panel).
2. Released a module to detect somatic mutations, genes and pathways driving to cancer based on exome sequencing data. See detail here
3. Fixed a number of potential bugs.
|
| 05/29/2013 |
| Add a variant-level QC tag, --vcf-filter-in, to use external QC function such as the Variant Quality Score Recalibration (VQSR) .
See detail here
|
| 05/25/2013 |
| Modified the definition of --gty-af-alt and add a QC tag --gty-af-het, which is critical for the de novo mutation scanning. See detail here
|
| 05/16/2013 |
| Extend the De novo mutation scanning function for multiple independent families or pedigrees at a time.
|
| 04/23/2013 |
| Add an OMIM disease gene annotation function.
|
| 04/15/2013 |
| Add the ESP5600 dataset as reference dataset for filtration of known sequence variants (hg19_ESP6500AA and hg19_ESP6500EA).
|
| 04/08/2013 |
| Add the dbSNP137 dataset as reference dataset for filtration of known sequence variants (hg18_dbsnp137 and hg19_dbsnp137).
|
| 04/05/2013 |
1. Add a function to detect somatic mutation(s) using matched tumor and non-tumor samples.
2. Update the pathogenic prediction by the dbNSFP v2.0 and add at most 13 available functional impact scores to more accurately calculate pathogenic probability by Logistic Regression Model.
3. Refine the cancer driver prediction function by a more reasonable training dataset.
|
| 02/06/2013 |
| Add a function to predict "driver " somatic mutation for cancer by the 12 available functional impact scores from dbNSFP v2.0b4.
|
| 12/08/2012 |
Update the pathogenic prediction by the dbNSFP v2.0b4 and add at most 12 available functional impact scores to more accurately calculate pathogenic probability by Logistic Regression Model.
|
| 09/06/2012 |
Add a genotyper filter for the detection of de novo muations in trios
|
| 08/08/2012 |
Update from KGGSeq V0.2 to KGGSeq V0.3
1. Added a function to export genotypes in format into KGGSeq binary genotype format which can use much less space store phased genotypes of sequence with multiple alternative alleles (up to 3).
2. Improved the algorithm to map sequence variants to RefGene, which are quicker and more accurate.
3. Simplified the commands.
4. Re-wrote the user manual, which is much easier to read.
|
| 06/23/2012 |
Merge all library files into a single kggseq.jar. This facilitates the redistribution of kggseq.
|
| 06/13/2012 |
1. Add a function for outputting genotypes in Plink format and flexibly select the sequence variants according to allele frequencies. This would be useful for QC checking by using Plink http://pngu.mgh.harvard.edu/~purcell/plink/ibdibs.shtml.
2. Use a new training dataset, ExoVar, to predict disease-causal nsSNVs.
3. Integrate a public variants dataset from NHLBI GO Exome Sequencing Project (ESP, http://evs.gs.washington.edu/EVS/) for variants filtration.
|
| 05/07/2012 |
Update the deleteriousness scores from dbNSFP 2.0, http://sites.google.com/site/jpopgen/dbNSFP.
|
| 03/15/2012 |
Add the protein features from http://www.uniprot.org/ and reference variants 1000g2012feb, dbSNP132 and dbSNP135 in hg19.
|
| 02/15/2012 |
Integrate the available Uniprot protein domains to annotate amino acid changes.
|
| 12/02/2011 |
Provide a Commands Generator with graphic interface for kggseq.
|
| 09/12/2011 |
Add a function to convert the VCF format into a format which can be recognized by kggseq as local filters (--local-filter).
|
| 08/25/2011 |
Release the first formal version of KGGSeq after extensive testing.
|
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Miao-xin Li, Precision Medical Genomics Laboratory, All rights reserved.
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