This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
☆22Mar 9, 2020Updated 6 years ago
Alternatives and similar repositories for gatk4-mitochondria-pipeline
Users that are interested in gatk4-mitochondria-pipeline are comparing it to the libraries listed below
Sorting:
- ☆15Apr 10, 2024Updated last year
- ☆14Oct 29, 2021Updated 4 years ago
- ☆12Nov 23, 2020Updated 5 years ago
- A tool set to assess the quality of the per read phasing and reduce the errors.☆13Jun 25, 2020Updated 5 years ago
- 🍶 Genome assembly with short sequence reads☆25Jan 21, 2024Updated 2 years ago
- Toolkit for calling and analyzing de novo STR mutations☆17Dec 17, 2023Updated 2 years ago
- Fork of ricopili for development of pipeline for family-based data☆19Jun 22, 2025Updated 8 months ago
- A series of tools and pipelines for genotyping MHC / HLA genes and alleles using SMRT Sequencing☆22Aug 29, 2016Updated 9 years ago
- mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data☆40Sep 8, 2025Updated 6 months ago
- ☆23Mar 20, 2024Updated last year
- mtDNA Variant Caller☆35Dec 23, 2024Updated last year
- Integrative analysis of complex structural variants☆22Sep 7, 2020Updated 5 years ago
- a tool for predicting mitochondrial DNA deletions using soft-clipping☆23Feb 3, 2022Updated 4 years ago
- Infer the age of ancestral nodes in a tree sequence.☆25Updated this week
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 3 months ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 6 months ago
- Probabilistic single-individual haplotyping☆10Mar 15, 2019Updated 6 years ago
- Detecting NUMTs from WGS☆13Nov 19, 2023Updated 2 years ago
- Tool for Motif Deconvolution in large HLA-II ligand datasets without the need of prior alignment.☆15Feb 17, 2025Updated last year
- phy-mer☆11Oct 12, 2017Updated 8 years ago
- ☆11Jul 13, 2018Updated 7 years ago
- Deduplication for cfDNA sequencing data☆11Jul 5, 2017Updated 8 years ago
- ☆11Mar 4, 2025Updated last year
- A bioinformatics pipeline to analyze mtDNA from NGS data☆97Mar 5, 2024Updated 2 years ago
- a hidden Markov model to infer simple repeats from genome sequences☆37Feb 19, 2021Updated 5 years ago
- Workflow Description Language - Specification and Implementations☆27Mar 19, 2019Updated 6 years ago
- Accompanying analysis code for the FRASER manuscript☆25Aug 27, 2020Updated 5 years ago
- Pipeline for structural variation detection in cohorts☆52Sep 14, 2021Updated 4 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆79Mar 9, 2020Updated 6 years ago
- ☆12Jul 4, 2022Updated 3 years ago
- ☆12Sep 4, 2022Updated 3 years ago
- Ascertained Sequentially Markovian Coalescent☆15Oct 22, 2025Updated 4 months ago
- ☆13Sep 11, 2025Updated 5 months ago
- Script used to identify de novo variants from sequencing data.☆11Mar 2, 2017Updated 9 years ago
- Tests Allelic Expression data for extreme imbalance w.r.t. population☆11Oct 8, 2021Updated 4 years ago
- WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.☆13Nov 18, 2025Updated 3 months ago
- Scripts for analyses and figures for SNP STR Imputation manuscript☆14Jul 24, 2018Updated 7 years ago
- A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples.☆13Feb 23, 2021Updated 5 years ago
- A collection of utilities for working with next generation (MPS) sequencing data in Groovy☆15Mar 2, 2026Updated last week