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SomaticQC tool help

SomaticQC (0.1-606-g0e1e89d)

Calculates QC metrics based on tumor-normal pairs.

SomaticQC integrates the output of the other QC tools and adds several metrics specific for tumor-normal pairs. The genome build form the settings file will be used during calcuation of QC metrics. All tools produce qcML, a generic XML format for QC of -omics experiments, which we adapted for NGS.

Mandatory parameters:
  -tumor_bam <file>   Input tumor bam file.
  -normal_bam <file>  Input normal bam file.
  -somatic_vcf <file> Input somatic vcf file.
  -out <file>         Output qcML file. If unset, writes to STDOUT.

Optional parameters:
  -links <filelist>   Files that appear in the link part of the qcML file.
                      Default value: ''
  -target_bed <file>  Target file used for tumor and normal experiment.
                      Default value: ''
  -skip_plots         Skip plots (intended to increase speed of automated tests).
                      Default value: 'false'

Special parameters:
  --help              Shows this help and exits.
  --version           Prints version and exits.
  --changelog         Prints changeloge and exits.
  --tdx               Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.

SomaticQC changelog

SomaticQC 0.1-606-g0e1e89d

2017-01-16 Increased speed for mutation profile, removed genome build switch.
2016-08-25 Version used in the application note.

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