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MGP1000

MGP1000

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
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Table of Contents

Overview

Bird’s-eye view of the pipeline

Preprocessing Module

Perform paired-end read data preprocessing according to best practices

Germline Module

Perform germline variant analyais, calling SNPs and InDels and estimate the ancestral admixture of each sample

Somatic Module

Perform matched tumor/normal somatic variant analyais, calling SNVs, InDels, CNVs, and SVs with consensus mechanism

Output Files

View a description of the output files for each module. Further detail of each output file format and some potential intended downstream usage is found in the Provenance for each module.