{"repo":"nf-core/variantbenchmarking","free":true,"listed":false,"github":"https://github.com/nf-core/variantbenchmarking","clone":"git clone https://github.com/nf-core/variantbenchmarking.git","description":"Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research","language":"Nextflow","stars":51,"topics":["benchmark","variant-calling","structural-variants","nextflow","nf-core","pipeline","workflow","small-variants"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/variantbenchmarking is designed to evaluate and validate the accuracy of variant calling methods in genomic research. Initially, the pipeline is tuned well for available gold standard truth sets (for example, Genome in a Bottle and SEQC2 samples) but it can be used to compare any two variant calling results. The workflow provides benchmarking tools for small variants including SNVs and INDELs, Structural Variants (SVs) and Copy Number Variations (CNVs) for germline and somatic analysis. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! The workflow involves several key processes to ensure reliable and reproducible results as follows: Standardization and normalization of test (query/comparison) variants: This initial step ensures consistent formatting and alignment of variants in test and truth VCF files for accurate comparison. - Subsample if input vcf is multisample (bcftools view) - Homogenization of multi-allelic variants, MNPs an","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/variantbenchmarking/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}