Skip to content

Latest commit

 

History

History
48 lines (31 loc) · 1.25 KB

usage.md

File metadata and controls

48 lines (31 loc) · 1.25 KB

Usage information

Basic execution

This pipeline requires Nextflow and Singularity to be loaded/available.

To run the pipeline on the IKMB MedCluster, the following command should work:

nextflow run ikmb/vcf-concordance --vcf your_variants.vcf.gz --reference NA12878 --assembly hg38

The options are described in the following:

Options

--ref_version

Release version of GIAB to use (v3, v4 (default)). Note that 4.2.1 uses patch 14 of GRCh38; whereas 3.3.1 is based on an older version.

--vcf

A gzipped, indexed (!) VCF file to be benchmarked.

--reference

The ID of a Genome-in-a-Bottle reference. Valid options are:

  • NA12878
  • NA24143
  • NA24149
  • NA24385
  • NA24631
  • NA24694
  • NA24695

--bed

A Bed file of e.g. your captured targets (exomes, panels). If you do not want to limit the analysis to any particular region(s), just leave this option empty.

--assembly

The human genome build to use. The default option is hg38 - other options are not currently configured.

Expert options

--ref_vcf

A gzipped, indexed VCF file to benchmark against (usually a Genome-in-a-Bottle sample)

--ref_bed

A bed file with high-confidence calling intervals in your reference (included with every GIAB data set)