C++ library and cmdline tools for parsing and manipulating VCF files
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Feb 17, 2021 - C++
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variant-calling
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Python library to facilitate genome assembly, annotation, and comparative genomics
bioinformatics
genomics
assembly
blast
comparative-genomics
variant-calling
synteny
sequence-alignments
genome-sequencing
genetic-maps
jcvi
allmaps
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Apr 19, 2021 - Python
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Jan 20, 2021 - Perl
Bayesian haplotype-based mutation calling
bioinformatics
genomics
somatic-variants
haplotypes
variants
variant-calling
single-cell
phasing
de-novo-mutation
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May 17, 2021 - C++
A tool set for short variant discovery in genetic sequence data.
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May 4, 2021 - C
Viral genomics analysis pipelines
genomics
genome
variant-calling
bam
genome-sequencing
illumina
fastq
genome-assembly
variant-annotations
viral-ngs
viral
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Nov 3, 2020 - Python
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
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Nov 4, 2020 - Python
Fast and accurate gene fusion detection from RNA-Seq data
rna-seq
cancer
gene-fusion
star
variant-calling
virus-integration
structural-variation
fusion-genes
gene-fusions
fusion-gene
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Apr 19, 2021 - C++
Graph realignment tools for structural variants
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Apr 16, 2021 - C++
De novo genome assembly and multisample variant calling
genomics
variant-calling
kmer
cortex
genome-analysis
genome-assembly
de-bruijn-graphs
genome-graph
contigs
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Mar 28, 2019 - C
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Apr 7, 2021 - Python
De novo assembly based variant calling pipeline for Illumina short reads
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Nov 30, 2020 - TeX
PacBio® variant and consensus caller
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Apr 25, 2019 - Python
public-health
report
variant-calling
bacteria
fastq
phylogenomics
denovo-assembly
genotyping
resistome
virulome
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Aug 3, 2020 - Perl
P.E.P.P.E.R.: Program for Evaluating Patterns in Pileups of Erroneous Reads
nanopore
variants
variant-calling
oxford-nanopore
genome-variation
long-reads
pacbio-ccs
assembly-polishing
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Mar 8, 2021 - Python
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
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May 17, 2021 - Python
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
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Apr 26, 2021
Genome inference from a population reference graph
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May 18, 2021 - C++
xHLA: Fast and accurate HLA typing from short read sequence data
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Oct 11, 2018 - Jupyter Notebook
A method for variant graph genotyping based on exact alignment of k-mers
ngs
bayesian-inference
variant-calling
indels
gibbs-sampling
structural-variation
snvs
dna-sequencing
genotyping
k-mers
variant-graphs
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Apr 1, 2019 - C++
GATK RNA-Seq Variant Calling in Nextflow
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Nov 1, 2020 - Nextflow
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
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Apr 5, 2021 - C++
Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.
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May 14, 2021 - C++
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
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Jan 18, 2019 - C++
SHuang-Broad
commented
Mar 2, 2021
Currently not all callers in our pipeline outputs vcf.gz.
To provide a unified "UI", we'd better zip all of them.
Need to work on (basically all SV VCFs)
- pbsv
- svim
- cutesv
- sniffles
- paftools
Assembly and intrahost/low-frequency variant calling for viral samples
workflow
nanopore
virus
pipeline
nextflow
assembly
metagenomics
variant-calling
illumina
oxford-nanopore
amplicon
viral
ont
nf-core
long-read-sequencing
artic
covid-19
covid19
sars-cov-2
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May 13, 2021 - Nextflow
A tool for fast and accurate summarizing of variant calling format (VCF) files
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Oct 1, 2020 - Python
find large indels (in the blind spot between GATK/freebayes and SV callers)
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Dec 3, 2017 - Nim
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It would be nice to add a params to choose the VEP genome assembly.
In most cases it is the
--genomeparams, but I'm assuming it'll be easier to control if we have that as a separate params.For example, it's currently not working with the
--genome customsetting.