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The Top 23 Perl Vcf Open Source Projects

Open source projects categorized as Perl Vcf
Vcftools ⭐ 415
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
most recent commit a year ago
Snippy ⭐ 408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
most recent commit 6 months ago
Vcf2maf ⭐ 305
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
most recent commit a year ago
Learning_vcf_file ⭐ 122
Learning the Variant Call Format
most recent commit 7 months ago
Ldblockshow ⭐ 102
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
most recent commit 7 months ago
Snpgenie ⭐ 94
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
most recent commit 8 months ago
23andme2vcf ⭐ 82
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
most recent commit 5 years ago
Simug ⭐ 58
simuG: a general-purpose genome simulator
most recent commit 2 years ago
Snpsplit ⭐ 43
Allele-specific alignment sorting
most recent commit a year ago
Novograph ⭐ 36
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
most recent commit 3 years ago
Circleator ⭐ 32
Flexible circular visualization of genome-associated data with BioPerl and SVG.
most recent commit 5 years ago
Isown ⭐ 28
most recent commit 4 years ago
Biotoolbox ⭐ 27
Tools for querying and analysis of genomic data
most recent commit 7 months ago
Evalsvcallers ⭐ 27
Evaluate the performances (precision and recall) of structural variation (SV) callers
most recent commit 5 months ago
Qc3 ⭐ 27
QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
most recent commit 8 years ago
16gt ⭐ 26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
most recent commit 4 years ago
Variant Filter ⭐ 25
A false-positive filter for variants called from massively parallel sequencing
most recent commit 7 years ago
Cgppindel ⭐ 25
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
most recent commit a year ago
Nb_distribution ⭐ 20
novoBreak: local assembly for breakpoint detection in cancer genomes
most recent commit 6 years ago
Bsa ⭐ 20
Bulked-Segregant Analysis using vcf file with or without parents
most recent commit 10 months ago
Ekidna ⭐ 19
Assembly based core genome SNP alignments for bacteria
most recent commit 5 years ago
Sift4g_create_genomic_db ⭐ 18
Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
most recent commit 7 months ago
Garfield Ngs ⭐ 16
GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS
most recent commit 5 years ago
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