An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
Usage:
The typical command for running the pipeline is as follows:
nextflow run nf-core/sarek --input sample.tsv -profile docker
Mandatory arguments:
--input Path to input TSV file on mapping, recalibrate and variantcalling steps
Multiple TSV files can be specified with quotes
This is a companion discussion topic for the original entry at github.com/nf-core/sarek