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germline

Here are 12 public repositories matching this topic...

dellytools / delly

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DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

c-plus-plus bam-files genome tumor cancer-genomics bioconda germline structural-variation svs delly-users genomic rearrangement delly sv-discovery deli delly-discussion-group

Updated Jul 23, 2021
C++

Sarek

SciLifeLab / Sarek

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Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

docker workflow bioinformatics pipeline genomics nextflow cancer somatic-variants reproducible-research containers next-generation-sequencing singularity badge reproducible-science travis-link somatic germline scilifelab gitter-badge germline-variants gitter-link scilifelab-link nextflow-link nbis-link ngi-link

Updated Jan 27, 2020
Nextflow

nf-core / sarek

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Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Updated Aug 6, 2021
Nextflow

sigven / gvanno

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Generic germline variant annotation pipeline

docker workflow gene database singularity vcf variants snv vep disease-gene-association indels annotation-tool vcfanno germline variant-annotations annotation-framework snvs germline-variants

Updated Aug 25, 2021
Python

pughlab / VisCap

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VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

copy-number-variation germline

Updated Dec 13, 2019
R

tobiasrausch / nRex

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nRex: Germline & Somatic single-nucleotide variant calling

somatic-variants sequencing mutations alignment variant-calling somatic-mutations germline

Updated Aug 9, 2021
Shell

antigenomics / segment-parser

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A parser for immune receptor gene data, mainly IMGT references

gene t-cell antibody germline immunoglobulin receptor imgt

Updated Jul 31, 2019
Groovy

AdamDS / 23AndMeAndClinVar

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Cross-reference 23andMe raw variant file with ClinVar

genetics snp clinvar germline 23andme

Updated Dec 30, 2017
Perl

EngLabGMI / germline_caya_solidtumor_analysis

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CAYA Analysis

genomics jupyter-notebook cancer-genomics cancer-research germline oncology ngs-analysis germline-variants maftools

Updated Apr 20, 2020
Jupyter Notebook

MBeyens / pyAmpli

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pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data

yaml bioinformatics genomics mips somatic-variants ngs variants amplicons germline ngstools variant-filtration targeted-sequencing haloplex

Updated Mar 25, 2021
Python

rosaak / germline_caya_solidtumor_analysis

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CAYA Analysis

jupyter-notebook cancer-genomics cancer-research germline oncology germline-variants childhood

Updated Aug 14, 2019
Jupyter Notebook

blazerroadg / react-native-azure-cosmos-gremlin

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This package provide rest api for azure cosmos germlin graph data base query access

react react-native reactjs azure germline azure-cosmos-db azure-cosmos

Updated Dec 6, 2020
C#

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