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The Top 23 Java Vcf Open Source Projects

Open source projects categorized as Java Vcf
Picard ⭐ 914
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
dependent packages 12total releases 176most recent commit 4 months ago
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78most recent commit 5 months ago
Rtg Tools ⭐ 260
RTG Tools: Utilities for accurate VCF comparison and manipulation
most recent commit 4 months ago
Gridss ⭐ 212
GRIDSS: the Genomic Rearrangement IDentification Software Suite
most recent commit a year ago
Genomewarp ⭐ 96
GenomeWarp translates genetic variants from one genome assembly version to another.
most recent commit 10 months ago
Hadoop Bam ⭐ 66
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
dependent packages 33total releases 17most recent commit 5 years ago
Haplogrep Cmd ⭐ 64
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
most recent commit a year ago
Jannovar ⭐ 51
Annotation of VCF variants with functional impact and from databases (executable+library)
dependent packages 5total releases 27most recent commit 4 months ago
Gor ⭐ 37
GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.
most recent commit 4 months ago
Hap Ibd ⭐ 35
The hap-ibd program detects identity-by-descent segments in phased genotype data.
most recent commit a year ago
Disq ⭐ 31
A library for manipulating bioinformatics sequencing formats in Apache Spark
dependent packages 3total releases 10most recent commit 8 months ago
Mutserve ⭐ 29
mtDNA Variant Caller
most recent commit 4 months ago
Varianttoolchest ⭐ 20
VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerful tools: (1) SetOperator for performing powerful set operations; and (2) VarStats for various statistics on VCF files.
most recent commit 8 years ago
Useq ⭐ 17
180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.
most recent commit 4 months ago
Sprime ⭐ 12
The SPrime program identifies variants that are introgressed from archaic populations.
most recent commit 2 years ago
Aperture ⭐ 12
Alignment-free detection of structural variations and viral integrations in circulating tumor DNA
most recent commit 2 years ago
Hadoopcnv ⭐ 12
HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data
most recent commit 7 years ago
Iris ⭐ 11
A module for improving the insertion sequences of structural variant calls
most recent commit 3 years ago
Wtchg Rg ⭐ 10
Reliable Genome project
most recent commit 7 years ago
Varitas ⭐ 9
Variant analysis with rapid incorporation of tabular annotation sources
most recent commit 9 years ago
Personal Sync Service ⭐ 8
This project aims to provide a SyncAdapter and a matching Server so you can manage and sync your contacts yourself
most recent commit 4 years ago
Bamscope ⭐ 7
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments.
most recent commit 4 months ago
Ipat ⭐ 7
iPat allows you to perform GWAS and GS with drags and clicks!
most recent commit 4 years ago
The 5 Most Depended On Java Vcf Open Source Projects
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 5 months ago
Picard ⭐ 914
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
dependent packages 12total releases 176latest release November 14, 2023most recent commit 4 months ago
Jannovar ⭐ 51
Annotation of VCF variants with functional impact and from databases (executable+library)
dependent packages 5total releases 27latest release September 13, 2022most recent commit 4 months ago
Disq ⭐ 31
A library for manipulating bioinformatics sequencing formats in Apache Spark
dependent packages 3total releases 10latest release February 09, 2021most recent commit 8 months ago
The 5 Latest Releases In Java Vcf Open Source Projects
Picard ⭐ 914
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
dependent packages 12total releases 176latest release November 14, 2023most recent commit 4 months ago
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 5 months ago
Jannovar ⭐ 51
Annotation of VCF variants with functional impact and from databases (executable+library)
dependent packages 5total releases 27latest release September 13, 2022most recent commit 4 months ago
Disq ⭐ 31
A library for manipulating bioinformatics sequencing formats in Apache Spark
dependent packages 3total releases 10latest release February 09, 2021most recent commit 8 months ago
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