vardict_filter_single-sample 0.1.5

• CWL specification 1.0

• Use example_inputs_single_filter.yaml to see the inputs to the cwl

• Example Command using toil:

    > toil-cwl-runner pv_vardict_single_filter.cwl example_inputs_single_filter.yaml

If at MSK, using the JUNO cluster having installed toil-msk version 3.21.1 you can use the following command

#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/pv_vardict_single_filter.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
> toil-cwl-runner --singularity --logFile /path/to/pv_vardict_single_filter_toil.log  --jobStore /path/to/pv_vardict_single_filter_jobStore --batchSystem lsf --workDir /path/to/pv_vardict_single_filter_toil_log --outdir . --writeLogs /path/to/pv_vardict_single_filter_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --disableChaining --maxLogFileSize 20000000000 /path/to/pv_vardict_single_filter_0.7.17.cwl /path/to/inputs.yaml > pv_vardict_single_filter_toil.stdout 2> pv_vardict_single_filter_toil.stderr &

Usage

Usage: pv vardict single filter [OPTIONS]

  This tool helps to filter vardict version 1.4.6 VCFs for single sample
  calling

Options:
  -i, --inputVcf FILE             Input vcf generated by vardict which needs
                                  to be processed  [required]
  --tsampleName TEXT              Name of the tumor Sample  [required]
  -dp, --totalDepth INTEGER RANGE
                                  Tumor total depth threshold  [default: 20;
                                  x>=20]
  -ad, --alleledepth INTEGER RANGE
                                  [x>=1]
  -tnr, --tnRatio INTEGER         Tumor-Normal variant fraction ratio
                                  threshold  [default: 1]
  -vf, --variantFraction FLOAT    Tumor variant fraction threshold  [default:
                                  5e-05]
  -mq, --minQual INTEGER          Minimum variant call quality  [default: 0]
  -fg, --filterGermline           Whether to remove calls without 'somatic'
                                  status
  -o, --outDir TEXT               Full Path to the output dir
  --help                          Show this message and exit.