All Projects → learning_vcf_file → Similar Projects or Alternatives

59 Open source projects that are alternatives of or similar to learning_vcf_file

vcfstats
Powerful statistics for VCF files
Stars: ✭ 32 (-69.23%)
Mutual labels:  vcf, vcf-files
spark-vcf
Spark VCF data source implementation for Dataframes
Stars: ✭ 15 (-85.58%)
Mutual labels:  vcf, vcf-files
SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Stars: ✭ 81 (-22.12%)
Mutual labels:  vcf, vcf-files
vcf stuff
📊Evaluating, filtering, comparing, and visualising VCF
Stars: ✭ 19 (-81.73%)
Mutual labels:  vcf
CuteVCF
simple viewer for variant call format using htslib
Stars: ✭ 30 (-71.15%)
Mutual labels:  vcf
laravel-vcard
A fluent builder class for vCard files.
Stars: ✭ 29 (-72.12%)
Mutual labels:  vcf
rvtests
Rare variant test software for next generation sequencing data
Stars: ✭ 114 (+9.62%)
Mutual labels:  vcf-files
vembrane
vembrane filters VCF records using python expressions
Stars: ✭ 46 (-55.77%)
Mutual labels:  vcf
Variants2Neoantigen
A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
Stars: ✭ 27 (-74.04%)
Mutual labels:  vcf
csv2vcf
🔧 Simple script in python to convert CSV files to VCF
Stars: ✭ 66 (-36.54%)
Mutual labels:  vcf
bioSyntax-archive
Syntax highlighting for computational biology
Stars: ✭ 16 (-84.62%)
Mutual labels:  vcf
cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
Stars: ✭ 85 (-18.27%)
Mutual labels:  vcf
Hap.py
Haplotype VCF comparison tools
Stars: ✭ 249 (+139.42%)
Mutual labels:  vcf
Snippy
✂️ ⚡️ Rapid haploid variant calling and core genome alignment
Stars: ✭ 245 (+135.58%)
Mutual labels:  vcf
Cyvcf2
cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (+133.65%)
Mutual labels:  vcf
Vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Stars: ✭ 229 (+120.19%)
Mutual labels:  vcf
Htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
Stars: ✭ 220 (+111.54%)
Mutual labels:  vcf
Survivor
Toolset for SV simulation, comparison and filtering
Stars: ✭ 180 (+73.08%)
Mutual labels:  vcf
Pcgr
Personal Cancer Genome Reporter (PCGR)
Stars: ✭ 168 (+61.54%)
Mutual labels:  vcf
Biosyntax
Syntax highlighting for computational biology
Stars: ✭ 164 (+57.69%)
Mutual labels:  vcf
Vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Stars: ✭ 126 (+21.15%)
Mutual labels:  vcf
Genomics
A collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (-2.88%)
Mutual labels:  vcf
Paragraph
Graph realignment tools for structural variants
Stars: ✭ 92 (-11.54%)
Mutual labels:  vcf
Truvari
Structural variant toolkit for VCFs
Stars: ✭ 85 (-18.27%)
Mutual labels:  vcf
Svtyper
Bayesian genotyper for structural variants
Stars: ✭ 79 (-24.04%)
Mutual labels:  vcf
Mixerp.net.vcards
vCard Serializer and Parser for C#
Stars: ✭ 56 (-46.15%)
Mutual labels:  vcf
Genozip
Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too
Stars: ✭ 53 (-49.04%)
Mutual labels:  vcf
16gt
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Stars: ✭ 26 (-75%)
Mutual labels:  vcf
Tiledb Vcf
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Stars: ✭ 26 (-75%)
Mutual labels:  vcf
Gvanno
Generic germline variant annotation pipeline
Stars: ✭ 23 (-77.88%)
Mutual labels:  vcf
Helmsman
highly-efficient & lightweight mutation signature matrix aggregation
Stars: ✭ 19 (-81.73%)
Mutual labels:  vcf
Hail
Scalable genomic data analysis.
Stars: ✭ 706 (+578.85%)
Mutual labels:  vcf
Htslib
C library for high-throughput sequencing data formats
Stars: ✭ 529 (+408.65%)
Mutual labels:  vcf
Vcard
This vCard PHP library can easily parse or generate/export vCards as .vcf
Stars: ✭ 333 (+220.19%)
Mutual labels:  vcf
Pygeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+150.96%)
Mutual labels:  vcf
Vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Stars: ✭ 259 (+149.04%)
Mutual labels:  vcf
VCF-kit
VCF-kit: Assorted utilities for the variant call format
Stars: ✭ 94 (-9.62%)
Mutual labels:  vcf
23andme2vcf
convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf
Stars: ✭ 91 (-12.5%)
Mutual labels:  vcf
telegram-json-to-vcf
Convert Telegram Contacts JSON File to VCF File
Stars: ✭ 34 (-67.31%)
Mutual labels:  vcf
Ontologies
Home of the Genomic Feature and Variation Ontology (GFVO)
Stars: ✭ 16 (-84.62%)
Mutual labels:  vcf
TypeTE
Genotyping of segregating mobile elements insertions
Stars: ✭ 15 (-85.58%)
Mutual labels:  vcf
vcf2gwas
Python API for comprehensive GWAS analysis using GEMMA
Stars: ✭ 27 (-74.04%)
Mutual labels:  vcf
SVCollector
Method to optimally select samples for validation and resequencing
Stars: ✭ 20 (-80.77%)
Mutual labels:  vcf
jannovar
Annotation of VCF variants with functional impact and from databases (executable+library)
Stars: ✭ 42 (-59.62%)
Mutual labels:  vcf
cutevariant
A standalone and free application to explore genetics variations from VCF file
Stars: ✭ 61 (-41.35%)
Mutual labels:  vcf
vcf2tsv
Genomic VCF to tab-separated values
Stars: ✭ 27 (-74.04%)
Mutual labels:  vcf
fuc
Frequently used commands in bioinformatics
Stars: ✭ 23 (-77.88%)
Mutual labels:  vcf
ilus
A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
Stars: ✭ 64 (-38.46%)
Mutual labels:  vcf
cpsr
Cancer Predisposition Sequencing Reporter (CPSR)
Stars: ✭ 44 (-57.69%)
Mutual labels:  vcf
indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
Stars: ✭ 38 (-63.46%)
Mutual labels:  vcf
snps
tools for reading, writing, merging, and remapping SNPs
Stars: ✭ 57 (-45.19%)
Mutual labels:  vcf
2vcf
convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations
Stars: ✭ 42 (-59.62%)
Mutual labels:  vcf
calcardbackup
calcardbackup: moved to https://codeberg.org/BernieO/calcardbackup
Stars: ✭ 67 (-35.58%)
Mutual labels:  vcf
sentieon-dnaseq
Sentieon DNAseq
Stars: ✭ 18 (-82.69%)
Mutual labels:  gatk
TeamTeri
Genomics using open source tools, running on GCP or AWS
Stars: ✭ 30 (-71.15%)
Mutual labels:  gatk
alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
Stars: ✭ 19 (-81.73%)
Mutual labels:  gatk
ngs pipeline
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Stars: ✭ 40 (-61.54%)
Mutual labels:  gatk
starfish
Intersect multiple VCF files with haplotype awareness
Stars: ✭ 19 (-81.73%)
Mutual labels:  vcf-files
phenomenet-vp
A phenotype-based tool for variant prioritization in WES and WGS data
Stars: ✭ 31 (-70.19%)
Mutual labels:  vcf-files
1-59 of 59 similar projects