GATK4 RNA variant calling pipeline

Assembly and intrahost/low-frequency variant calling for viral samples

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...

This implementation was done for the ELIXIR EXCELERATE Demonstrator to be run on WES-TES environment.

There is also task related to input file transfer (curl) and the output file transfer to a private FTP server. The needed URLs and FTP credential are given as input parameters.

The input files are assumed to come from a web server. Idea there is to make some configurations more modular and some tools like lftp or curl have easier to write script parameter files instead of command line parameters. ...

nf-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. ...