|
Python |
3 |
Snakemake pipeline for variant calling using GATK |
Mar 02, 2023 |
|
Nextflow |
2 |
Somatic variant calling pipeline using Mutect2 adapted from GATK Best Practices |
Jul 08, 2019 |
|
Scala |
3 |
GATK QScripts used in our illumina variant calling pipeline. |
Jul 22, 2016 |
|
Shell |
2 |
A shell script which implements GATK pipeline for variant calling. |
Nov 29, 2023 |
|
Ruby |
2 |
Pipeline to run BWA + GATK on a Illumina sample. |
Feb 26, 2022 |
|
Python |
18 |
Variant annotation and merging pipeline |
Feb 23, 2023 |
|
Shell |
4 |
H3A variant calling pipeline |
Apr 20, 2021 |
|
Jupyter Notebook |
4 |
Pipeline for variant annotation using Variant Effect Predictor (VEP) |
Nov 30, 2023 |
|
Jupyter Notebook |
4 |
A bioinformatic variant calling pipeline |
Aug 24, 2017 |
|
Nextflow |
9 |
gatk4 RNA variant calling pipeline |
Aug 02, 2022 |
|
Shell |
11 |
NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC |
Apr 06, 2022 |
|
None |
5 |
SNP and variant calling pipeline for bacteria |
Feb 02, 2023 |
|
C |
10 |
TOPMed Freeze 3 variant calling pipeline |
Nov 24, 2021 |
|
Shell |
20 |
Variant Calling Pipeline in Cromwell/WDL |
Nov 13, 2020 |
|
Python |
2 |
Snakemake pipeline for read mapping and variant calling |
Sep 08, 2022 |
|
R |
5 |
Automated Pipeline for Variant/Haplotype Calling and Filtering |
May 13, 2023 |
|
Python |
41 |
Generic human DNA variant annotation pipeline |
Apr 27, 2023 |
|
Perl |
2 |
The Ensembl gene annotation pipeline (a work in progress) |
Apr 19, 2022 |
|
Python |
3 |
An empirical variant annotation and data evaluation pipeline. |
Jan 12, 2022 |
|
Jupyter Notebook |
22 |
SARS-CoV-2 variant calling and consensus assembly pipeline |
Apr 28, 2023 |
|
R |
2 |
Wrapper and analysis scripts for RNA variant calling pipeline |
Nov 19, 2023 |
|
None |
3 |
Perform bwa alignment and pre-processing following GATK best practices |
Aug 24, 2017 |
|
Nextflow |
186 |
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS … |
Aug 16, 2022 |
|
Python |
5 |
Andersen Lab Python-based pipeline for variant calling. |
Jan 28, 2023 |
|
Nextflow |
3 |
Variant calling pipeline for the Illumina Dragen platform |
Apr 17, 2023 |
|
Nextflow |
7 |
MNase-seq analysis pipeline using BWA and DANPOS2. |
May 25, 2022 |
|
Nextflow |
12 |
Nextflow pipeline for Mutect2 somatic variant calling best practices |
Jul 14, 2022 |
|
Python |
3 |
Multisample DNAseq variant calling pipeline for use in diagnostics |
Mar 11, 2021 |
|
Python |
2 |
variant calling and processing |
Apr 27, 2022 |
|
Nextflow |
11 |
A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and … |
Jun 23, 2022 |
|
Nextflow |
7 |
Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices |
Dec 11, 2021 |
|
Nextflow |
2 |
Germline structural variant calling pipeline for short read WGS datasets |
Jul 13, 2023 |
|
Nextflow |
37 |
Simple bacterial assembly and annotation pipeline |
Aug 09, 2022 |
|
Python |
29 |
10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling |
Feb 15, 2023 |
|
Shell |
2 |
Variant calling and PSMC workflows |
Oct 22, 2023 |
|
Python |
2 |
A Pipeline for comparing GATK and Deepvariant |
Nov 05, 2023 |
|
Python |
66 |
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads. |
Apr 14, 2023 |
|
TeX |
101 |
De novo assembly based variant calling pipeline for Illumina short reads |
Aug 12, 2022 |
|
wdl |
6 |
WDL workflows for variant calling and assembly using ONT |
Apr 19, 2023 |
|
wdl |
44 |
This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best … |
Jan 28, 2023 |
|
wdl |
2 |
This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best … |
Aug 08, 2019 |
|
C++ |
103 |
Genome browser and variant annotation |
May 17, 2023 |
|
R |
6 |
Build Annotation package by using information from KEGG, NCBI, Ensembl |
Apr 18, 2023 |
|
Nextflow |
4 |
Nextflow pipeline for BWA, BWA2 and STAR alignments |
May 07, 2022 |
|
None |
2 |
Consensus assembly and variant calling workflow |
Aug 17, 2017 |
|
None |
15 |
Minor Variant Calling and Phasing Tools |
Jul 31, 2022 |
|
None |
12 |
Consensus assembly and variant calling workflow. |
Oct 27, 2022 |
|
JavaScript |
61 |
Reference-based variant calling pipeline for a pair of phased haplotype assemblies |
Jul 22, 2022 |
|
R |
2 |
Example variant calling workflow using R targets package |
Jan 31, 2023 |
|
R |
98 |
Copy number calling and variant classification using targeted short read sequencing |
Apr 25, 2023 |