Precision HLA typing from next-generation sequencing data using OptiType.
Table of Contents
Introduction
Quick Start
With Docker
With Singularity
Documentation
Pipeline DAG
Input fastq
Input bam
Credits
Introduction
OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are
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Downloadnf-core/deepvariant
Deep Variant as a Nextflow pipeline
A Nextflow pipeline for running the Google DeepVariant variant caller.
What is DeepVariant and why in Nextflow?
The Google Brain Team in December 2017 released a Variant Caller based on DeepLearning: DeepVariant.
In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format.
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