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 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.