This is a problem I have to solve frequently, and I'd be interested in knowing what other methods people use to solve the same problem.About twice a year, I get asked to determine variants from Illumina reads, usually from either mouse or human. These are things that have good reference genomes (e.g. human genome from ensembl, mouse genome from ensembl), and are frequently tested out on various bioinformatics tools.I have at my disposal three computers, in order of usage preference: a laptop with 4 processing threads and 8GB of memory, a desktop with 12 processing threads and 64GB of memory, and a server with 24 processing threads and 256GB of memory. Occasionally I get access to better computers when I need to do lots of processing, or to do things quickly, but these comprise my basic bioinformatics team.I've had whole-genome projects that involved processing data from 4 individuals, up to projects with about 120 individuals, with each individual having about 10-40M paired-end reads (100-125bp each). Beyond this level, I suspect other researchers will typically have their own bioinformatics team and/or capabilities, which is why I don't get any of the larger-scale jobs that I hear about from salaried bioinformaticians.What is the standard approach that you would use to process these reads into reference-mapped variant data (i.e. gzipped VCF) for use in downstream analysis tools (e.g. VEP)?
How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?
variant calling;read mapping;human genome