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Search results for perl vcf
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vcf
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41 search results found
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.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Vcf2maf
⭐
305
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Learning_vcf_file
⭐
122
Learning the Variant Call Format
Ldblockshow
⭐
102
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
Snpgenie
⭐
94
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
23andme2vcf
⭐
82
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
Simug
⭐
58
simuG: a general-purpose genome simulator
Snpsplit
⭐
43
Allele-specific alignment sorting
Novograph
⭐
36
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
Circleator
⭐
32
Flexible circular visualization of genome-associated data with BioPerl and SVG.
Isown
⭐
28
Biotoolbox
⭐
27
Tools for querying and analysis of genomic data
Evalsvcallers
⭐
27
Evaluate the performances (precision and recall) of structural variation (SV) callers
Qc3
⭐
27
QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
16gt
⭐
26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Variant Filter
⭐
25
A false-positive filter for variants called from massively parallel sequencing
Cgppindel
⭐
25
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
Nb_distribution
⭐
20
novoBreak: local assembly for breakpoint detection in cancer genomes
Bsa
⭐
20
Bulked-Segregant Analysis using vcf file with or without parents
Ekidna
⭐
19
Assembly based core genome SNP alignments for bacteria
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.
Garfield Ngs
⭐
16
GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS
Parsecnv2
⭐
14
Parse Copy Number Variation from Array and Sequencing
Variantdb_challenge
⭐
14
Finding a scalable alternative to the VCF File for genomics analysis
Phasing
⭐
14
Evaluation of phasing performance
Typete
⭐
12
Genotyping of segregating mobile elements insertions
Forge
⭐
12
GWAS SNP Regulatory Analysis Tool
Microhaplot
⭐
11
microhaplotype visualizer and analyzer
Bioscripts
⭐
9
Scripts for bioinformatics data processing and analysis
Vcf Conversion Tools
⭐
8
Tools to convert to and from vcf format
Vafcorrect
⭐
8
Calculates the Variant Allele Fraction of variants in VCF files
Somaticwrapper
⭐
8
Detect somatic variants from tumor and normal WGS/WXS data
Combisv
⭐
7
Combine structural variation outputs from long sequencing reads into a superior call set
Popgen
⭐
7
Small scripts for population genetics analysis
Michigan Imputation Helper
⭐
6
Svparser
⭐
6
Explore and filter structural variant calls from Lumpy and Delly VCF files
Ebt
⭐
6
Evolutionary Bioinformatics Toolkit (EBT)
Exonchipprocessing
⭐
5
Ephagen
⭐
5
Estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum
Neoscan
⭐
5
predict neoantigen for indel and snvs
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