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SomaticQC tool help

SomaticQC (2024_08-110-g317f43b9)

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.
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/CRAM file.
  -normal_bam <file>   Input normal BAM/CRAM file.
  -somatic_vcf <file>  Input somatic VCF file.

Optional parameters:
  -out <file>          Output qcML file. If unset, writes to STDOUT.
                       Default value: ''
  -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: ''
  -target_exons <file> BED file containing target exons, neccessary for TMB calculation. Please provide a file that contains the coordinates of all exons in the reference genome.
                       Default value: ''
  -blacklist <file>    BED file containing regions which are ignored in TMB calculation.
                       Default value: ''
  -tsg_bed <file>      BED file containing regions of tumor suppressor genes for TMB calculation.
                       Default value: ''
  -ref <file>          Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                       Default value: ''
  -skip_plots          Skip plots (intended to increase speed of automated tests).
                       Default value: 'false'
  -build <enum>        Genome build used to generate the input.
                       Default value: 'hg38'
                       Valid: 'hg19,hg38'

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'.
  --settings [file]    Settings override file (no other settings files are used).

SomaticQC changelog

SomaticQC 2024_08-110-g317f43b9

2020-11-27 Added CRAM support.
2018-07-11 Added build switch for hg38 support.
2017-07-28 Added somatic allele frequency histogram and tumor estimate.
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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