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Tool and database overview

Databases general

database used for last update/check notes url
ClinGen pipeline 08.2024 (latest - not versioned) https://ftp.clinicalgenome.org/
RepeatMasker pipeline 08.2024 (140131) https://www.repeatmasker.org/species/hg.html
ClinVar (SNVs and CNVs) pipeline, NGSDImportHPO 08.2024 (20240805) update IGV custom tacks in GSvar https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2024/
HGNC pipeline, NGSDImportHGNC 08.2024 (latest - not versioned) https://ftp.ebi.ac.uk/pub/databases/genenames/
gnomAD (genome) pipeline 08.2024 (4.1) https://gnomad.broadinstitute.org/downloads
gnomAD (constraints) NGSDImportGeneInfo 08.2024 (2.1.1) v4 still contains no gonosomes: https://gnomad.broadinstitute.org/news/2024-03-gnomad-v4-0-gene-constraint/ https://gnomad.broadinstitute.org/downloads
phyloP pipeline 08.2024 (05.2015) https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/
CADD pipeline 08.2024 (1.7) https://cadd.gs.washington.edu/download
REVEL pipeline 08.2024 (1.3) https://sites.google.com/site/revelgenomics/downloads
AlphaMissense pipeline 08.2024 (03.08.2023) https://console.cloud.google.com/storage/browser/dm_alphamissense
OMIM pipeline, NGSDImportHPO 07.2023 (latest - not versioned) https://omim.org/downloads/
HGMD (SNVs and CNVs) pipeline 08.2024 (2024.2) update IGV custom tacks in GSvar https://apps.ingenuity.com/ingsso/login
Ensembl pipeline, NGSDImportEnsembl 08.2024 (GRCh38.112) update IGV genome https://ftp.ensembl.org/pub/release-112/gff3/homo_sapiens/
HPO NGSDImportHPO 08.2024 (2024-08-13) send updated HPO list to Anne (scripts/2021_10_21_hpo_update/) https://github.com/obophenotype/human-phenotype-ontology
GenCC NGSDImportHPO 08.2024 (latest - not versioned) https://search.thegencc.org/download
G2P NGSDImportHPO 08.2024 (14_6_2024) https://www.ebi.ac.uk/gene2phenotype/downloads/
ORPHA NGSDImportORPHA 08.2024 (latest - not versioned) Products 1 and 6 are updated tweice a year only (July and December) https://github.com/Orphanet

Databases for somatic pipelines

database used for last update/check notes url
CancerHotspots pipeline (somatic) 08.2024 version is final and does not change https://www.cancerhotspots.org
NCG7.1 pipeline (somatic) 08.2024 (v7.1) manually update data/gene_lists/somatic_tmb_tsg.bed if NCG file changes http://ncg.kcl.ac.uk/
COSMIC CMC pipeline (somatic) 08.2024 (v99) https://cancer.sanger.ac.uk/cmc
Human Protein Atlas pipeline (somatic) 08.2024 (v23) https://www.proteinatlas.org/about/download

Databases for RNA pipelines

database used for last update/check notes url
Ensembl GTF file pipeline (RNA) 08.2024 (kept on ensembl v109 gtf) Keep at V109 as the NGSD import is based on these transcripts - if updated also remake STAR index https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/

Tools general

tool used for last update/check notes url
ngs-bits annotation, quality control, ... 08.2024 (2024_07)
samtools BAM sorting 08.2024 (1.20) https://github.com/samtools/samtools/releases/
bwa2 mapping (default) 08.2024 (2.2.1) https://github.com/bwa-mem2/bwa-mem2
bwa mapping (if use_bwa1 is true in settings) 08.2024 (0.7.18) https://github.com/lh3/bwa/
samblaster duplicate removal 08.2024 (0.1.26) https://github.com/GregoryFaust/samblaster
abra2 indel realignment 08.2024 (2.23) skip 2.24 mozack/abra2#46 https://github.com/mozack/abra2
freebayes variant calling 08.2024 (1.3.6) skip 1.3.8 freebayes/freebayes#765, freebayes/freebayes#809 https://github.com/ekg/freebayes
vcflib VCF normalization 08.2024 (1.0.3) skip 1.0.9 vcflib/vcflib#398 https://github.com/vcflib/vcflib
ClinCNV CNV calling 08.2024 (1.18.3) https://github.com/imgag/ClinCNV
VEP annotation 08.2024 (112.0) https://github.com/Ensembl/ensembl-vep/releases
manta structural variant calling 08.2024 (1.6.0) https://github.com/Illumina/manta
InterOp reading InterOp metric files (Illumina NextSeq 1k/2k) 08.2024 (1.2.4) version 1.3.2 available but update not necessary https://github.com/Illumina/interop
Circos circos plot with CNVs,ROHS,etc 08.2024 (0.69.9) https://circos.ca/software/download/
ExpansionHunter Repeat expansion calling 08.2024 (5.0.0) https://github.com/Illumina/ExpansionHunter
SpliceAI Predict splicing variant effect 08.2024 (1.3.1) https://github.com/Illumina/SpliceAI
REViewer Repeat expansion visualization 08.2024 (0.2.7) https://github.com/Illumina/REViewer
GATK gVCF merging 08.2024 (4.6.0.0) https://github.com/broadinstitute/gatk/releases
ORAD Illumina ORA file decompression 08.2024 (2.6.1) version 2.7.0 available but update not necessary

Tools for somatic pipelines

tool somatic used for last update/check notes url
strelka2 variant calling (tumor/normal) 08.2024 (2.9.10) https://github.com/Illumina/strelka
msisensor-pro microsatelite instability (tumor/normal) 08.2024 (v1.2.0) https://github.com/xjtu-omics/msisensor-pro
varscan2 variant calling 08.2024 (2.4.6) https://github.com/dkoboldt/varscan
umiVar2 variant calling cfDNA 08.2024 (2024_07) https://github.com/imgag/umiVar2
hla-genotyper HLA genotyping 08.2024 (2022_05) https://github.com/axelgschwind/hla-genotyper
SigProfilerExtractor mutational signatures 08.2024 (1.1.24) https://github.com/AlexandrovLab/SigProfilerExtractor

Tools for RNA pipeline

tool RNA used for last update/check notes url
STAR mapping 08.2024 (2.7.11b) https://github.com/alexdobin/STAR
subread read counting 08.2024 (2.0.6) https://subread.sourceforge.net/
Arriba fusion detection 08.2024 (2.4.0) https://github.com/suhrig/arriba
Kraken2 fastq filtering 08.2024 (2.1.3) https://github.com/DerrickWood/kraken2
umi_tools UMI extraction 08.2024 (1.1.5) https://github.com/CGATOxford/UMI-tools

Tools for longread pipeline

tool longread used for last update/check notes url
minimap2 mapping 08.2024 (2.28) https://github.com/lh3/minimap2
clair3 small variant calling 08.2024 (1.0.10) https://github.com/HKU-BAL/Clair3
whatshap phasing (helper tool for clair3) 08.2024 (2.3) installed via pip in megSAP python environment https://github.com/whatshap/whatshap
pypy3 alt. python implementation (helper tool for clair3) 08.2024 (v7.3.16) https://www.pypy.org/
parallel tool to execute in parallel (helper tool for clair3) 08.2024 (20240722) https://www.gnu.org/software/parallel/
longphase phasing 08.2024 (v1.7.3) https://github.com/twolinin/longphase
sniffles structural variant calling 08.2024 (v2.4) installed via pip in megSAP python environment https://github.com/fritzsedlazeck/Sniffles
straglr repeat expansion caller 08.2024 (v1.5.1) https://github.com/bcgsc/straglr
Tandem Repeats Finder 08.2024 (v4.09.1) helper tool for straglr https://github.com/Benson-Genomics-Lab/TRF
Blastn 08.2024 (2.16.0) helper tool for straglr https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
straglrOn repeat expansion visualization 08.2024 (v0.2.2) TODO https://github.com/leonschuetz/StraglrOn
modkit methylation extraction 08.2024 (v0.3.2) https://github.com/nanoporetech/modkit