genetic variant expressions, annotation, and filtering for great good.
☆273Dec 15, 2025Updated 2 months ago
Alternatives and similar repositories for slivar
Users that are interested in slivar are comparing it to the libraries listed below
Sorting:
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆304Nov 14, 2025Updated 3 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- nim wrapper for htslib for parsing genomics data files☆157Dec 15, 2025Updated 2 months ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆264Jun 17, 2024Updated last year
- Plot structural variant signals from many BAMs and CRAMs☆560Jul 13, 2024Updated last year
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆828Feb 10, 2026Updated 3 weeks ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆52Apr 9, 2021Updated 4 years ago
- using all the bits for echt rapid variant annotation and filtering☆153Feb 18, 2026Updated 2 weeks ago
- cython + htslib == fast VCF and BCF processing☆430Feb 23, 2026Updated last week
- Structural variant toolkit for VCFs☆397Jan 23, 2026Updated last month
- useful command-line tools written to showcase hts-nim☆50Nov 10, 2020Updated 5 years ago
- a lightweight db framework for exploring genetic variation.☆326Apr 28, 2020Updated 5 years ago
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆58Feb 17, 2022Updated 4 years ago
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆132Oct 14, 2025Updated 4 months ago
- Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data☆75Sep 4, 2024Updated last year
- goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary☆225Sep 18, 2025Updated 5 months ago
- (WIP) best-practices workflow for rare disease☆62Jul 1, 2024Updated last year
- Annotation and Ranking of Structural Variation☆287Updated this week
- don't get DUP'ed or DEL'ed by your putative SVs.☆107Dec 14, 2020Updated 5 years ago
- Detect novel (and reference) STR expansions from short-read data☆70Dec 6, 2025Updated 3 months ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆147Feb 17, 2026Updated 2 weeks ago
- A tool for estimating repeat sizes☆206Jan 30, 2024Updated 2 years ago
- ☆18Mar 14, 2022Updated 3 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- prioritize effects of variant annotations from VEP, SnpEff, et al.☆34Dec 10, 2024Updated last year
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆506Feb 26, 2026Updated last week
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆279May 21, 2025Updated 9 months ago
- a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads☆212Oct 2, 2025Updated 5 months ago
- Runs a combination of tools to generate structural variant calls on whole-genome sequencing data☆103Nov 5, 2020Updated 5 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆338Feb 22, 2026Updated last week
- web-based analysis tool for rare disease genomics☆201Updated this week
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 3 weeks ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆536Feb 12, 2026Updated 3 weeks ago
- A Tool to Annotate and Prioritize Exome Variants☆241Feb 28, 2026Updated last week
- Scalable gVCF merging and joint variant calling for population sequencing projects☆177Apr 12, 2024Updated last year
- Structural variant and indel caller for mapped sequencing data☆460Oct 11, 2025Updated 4 months ago
- Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer☆21Dec 8, 2020Updated 5 years ago
- Smart VCF parser DSL☆83May 24, 2022Updated 3 years ago