TronFlow is an open source collection of computational workflows originally conceived for tumor-normal somatic variant calling over whole exome data and the manipulation of BAM and VCF files with the aim of having comparable and analysis-ready data. Over time, we have extended it to germline variant calling, copy numbers and other related technologies and analyses.
Its modular architecture covers different analytical and methodological use cases that allow analysing FASTQ files into analysis-ready ...
Maintainers: Pablo Riesgo Ferreiro
Number of items: 2
Tags: Alignment, Annotation, Nextflow, variant calling, VCF, Mutect2, HaplotyeCaller, Strelka2
CoVigator pipeline: variant detection pipeline for Sars-CoV-2
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StructuralVariants Workflow
Type: Nextflow
Creators: Laura Rodriguez-Navas, Adrián Muñoz-Civico, Daniel López-López
Submitter: Laura Rodriguez-Navas
StructuralVariants Workflow
Type: Common Workflow Language
Creators: Laura Rodriguez-Navas, Daniel López-López
Submitter: Laura Rodriguez-Navas
Bootstrapping-for-BQSR @ NCI-Gadi is a pipeline for bootstrapping a variant resource to enable GATK base quality score recalibration (BQSR) for non-model organisms that lack a publicly available variant resource. This implementation is optimised for the National Compute Infrastucture's Gadi HPC. Multiple rounds of bootstrapping can be performed. Users can use Fastq-to-bam @ NCI-Gadi and Germline-ShortV @ NCI-Gadi to ...
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