ngs-pl run-targeted-variant-caller

Synopsis

ngs-pl run-targeted-variant-caller -o/–outdir OUTDIR [–snakefile] [–panel] [-t/–target] [-p/–paired] [-s/–single] [-u/–underscore] INPUTFILES

Description

ngs-pl run-targeted-variant-caller runs targeted variant calling workflow to produce single-sample VCF file for each sample. Each VCF file will then be merged into a multi-sample VCF file when --target is set to merged_vcf.

Options

-h, --help

Show this help message and exit.

-o, --outdir OUTDIR

Output directory to create the symbolic links.

--debug

Enable debug mode for detailed logging.

--snakefile

Snakefile to use for the workflow. When supplied without absolute or relative path, the snakefile will be looked up from the available snakefiles included with the pipeline. See the configuration section below for the list of available snakefiles.

-t, --target

Set the target of the workflow. Available targets depend on the used snakefile, see the configuration section below.

Configurations

targeted_variant_caller_wf

Snakemake workflow file (snakefile) to run.

Available snakefiles are:

msf_panel_varcall_lr.smk

This is the workflow for panel variant calling using singleton long reads from ONT or PacBio.

Available targets are:

merged_vcf

This results in a multi-sample VCF file as VCF files from each sample is merged using bcftools merge command.

merged_report

This results in a Excel file containing report of genotypes of each sample.

msf_panel_varcall_pe.smk

This is the workflow panel variant calling using paired-end short reads from Illumina platforms.

Available targets are the same as msf_panel_varcall_lr.smk above

target

The targets will be specific to each of snakefile. See the snakefile above to get the available targets.