snvs

There are 1 repository under snvs topic.

Illumina / strelka
Strelka2 germline and somatic small variant caller
bioinformatics snvs indels snps
Language:C++ 350
sigven / pcgr
Personal Cancer Genome Reporter (PCGR)
cancer-genomics cancer-variants somatic interpreter reporting-engine clinical oncology-data precision-oncology vcf tumor annotation-framework annotation-tool cancer copy-number-variation snvs therapeutic-targets precision-cancer-medicine variant-interpretation
Language:R 247
nygenome / lancet
Microassembly based somatic variant caller for NGS data
somatic-mutations cancer-genomics variant-callers debruijn-graph snvs indels local-assembly
Language:C 153
bioinformatics-centre / BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
variant-calling genotyping ngs variant-graphs dna-sequencing snvs indels structural-variation bayesian-inference gibbs-sampling k-mers
Language:C++ 86
Illumina / PlatinumGenomes
The Platinum Genomes Truthset
variant-analysis snvs indels
84
KChen-lab / Monopogen
SNV calling from single cell sequencing
germline-variants single-cell snvs somatic-variants
Language:HTML 68
HKU-BAL / ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
deep-learning long-reads nanopore ont somatic-mutations somatic-variants bioinformatics genomics haplotypes phasing snvs indels illumina long-read-sequencing short-reads pacbio
Language:Python 60
sigven / gvanno
Generic human DNA variant annotation pipeline
docker gene vep vcfanno germline variant-annotations vcf snv indels annotation-framework annotation-tool workflow singularity snvs variants disease-gene-association
Language:Python 53
HKU-BAL / ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning genomics illumina long-read-sequencing long-reads nanopore ont pacbio snvs somatic-mutations somatic-variants tumor-only tumors variant-calling variants
Language:Python 37
zhixingfeng / iGDA
Detect and phase minor SNVs from long-read sequencing data
snvs oxford-nanopore pacbio-sequencing variants strains metagenome-deconvolution
Language:C++ 12
cpwardell / FiNGS
Filters for Next Generation Sequencing
sequencing ngs variants filtering snvs cancer cancer-genomics genomics
Language:Python 10
nalomran / PyReQTL
A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.
bioinformatics bioinformatics-analysis bioinformatics-tool python python3 pandas numpy scipy rpy2 r snvs gene-expression rna-seq rna-seq-analysis matrixeqtl data-science
Language:Python 10
DHQP / SNVPhyl_Nextflow
Nextflow version of SNVPhyl
snvs
Language:Nextflow 9
dbmi-bgm / granite
A collection of software to work with genomic variants
vcf variants variant-analysis trio de-novo-mutation compound-heterozygous de-novo-mutations variant-filtration snv snvs single-nucleotide-variation
Language:Python 6
hongenxu / MDV_proj
Scripts used in MDV project
perl snvs indels marek-disease
Language:Perl 4
CERC-Genomic-Medicine / WEGS_pipelines
Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.
gatk genetics indels sequencing snps snvs wegs wes wgs
Language:Nextflow 3
nickveltmaat / SNVcaller
Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
cell-free-dna cfdna ctdna indel lofreq mutect2 sinvict snv snv-annotation snvs somatic-mutations somatic-variants vardict
Language:Python 3
EichlerLab / aws
This is the github repository for the Eichler lab Amazon Web Services (AWS) pipelines
genome amazon qc snvs cnvs
Language:Perl 2
phdscripts
asw0049 / phdscripts
This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.
bash-scripting bioinformatics bioinformatics-pipeline ggplot2 scripts snps snvs temperature bwa-mem mitochondria mitochondrial-genomes mitochondrial-variants mutect2 samtools awk awk-script
Language:Shell 1
myonaung / sm-SNIPER
A snakemake pipeline that performs variant calling of Nanopore reads from FastQ files for non-model organisms
genomics bioinformatics-pipeline snakemake-workflows snvs variant variant-calling
Language:Python 1
tycheleturner / exome_class
Codes for exome sequencing class being taught by Tychele N. Turner, Ph.D.
exome class qc snvs cnvs gatk freebayes conifer xhmm
Language:R 1
tycheleturner / genome_class
Codes for genome sequencing class being taught by Tychele N. Turner, Ph.D.
genome class qc snvs cnvs
Language:R 1
j3551ca / SNPerr
Determine read depth and variant frequency thresholds to distinguish NGS sequencing errors from true SNPs. Simulates effect of changing per-site read depth and variant frequency on accuracy of genetic diversity measures (pi, alterante allele frequency, shannon diversity).
diversity error ngs snvs
Language:Python 0
poximan / covexcel
parser para planillas excel, sobre cargado de potenciales casos covid
excel parser covid argentina sisa snvs
Language:JavaScript 0
edawson / assisi
A somatic mutation signature simulator
mutational-signatures snvs simulation autoencoders
Language:Python
julianspaeth / snv-calling-workflow
SNV calling workflow
snps snvs makefile workflow bioinformatics
Language:Makefile