| 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 |
| 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 |
| 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/ |
| 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 |
| 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 |
| 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 |
| 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 |