Skip to content

Latest commit

 

History

History
58 lines (52 loc) · 3.19 KB

MappingQC.md

File metadata and controls

58 lines (52 loc) · 3.19 KB
Raw

MappingQC tool help

MappingQC (2024_08-110-g317f43b9)

Calculates QC metrics based on mapped NGS reads.

Mandatory parameters:
  -in <file>                 Input BAM/CRAM file.

Optional parameters:
  -out <file>                Output qcML file. If unset, writes to STDOUT.
                             Default value: ''
  -roi <file>                Input target region BED file (for panel, WES, etc.).
                             Default value: ''
  -wgs                       WGS mode without target region. Genome information is taken from the BAM/CRAM file.
                             Default value: 'false'
  -rna                       RNA mode without target region. Genome information is taken from the BAM/CRAM file.
                             Default value: 'false'
  -txt                       Writes TXT format instead of qcML.
                             Default value: 'false'
  -min_mapq <int>            Minmum mapping quality to consider a read mapped.
                             Default value: '1'
  -no_cont                   Disables sample contamination calculation, e.g. for tumor or non-human samples.
                             Default value: 'false'
  -debug                     Enables verbose debug outout.
                             Default value: 'false'
  -build <enum>              Genome build used to generate the input (needed for WGS and contamination only).
                             Default value: 'hg38'
                             Valid: 'hg19,hg38,non_human'
  -ref <file>                Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                             Default value: ''
  -cfdna                     Add additional QC parameters for cfDNA samples. Only supported mit '-roi'.
                             Default value: 'false'
  -somatic_custom_bed <file> Somatic custom region of interest (subpanel of actual roi). If specified, additional depth metrics will be calculated.
                             Default value: ''
  -read_qc <file>            If set, a read QC file in qcML format is created (just like ReadQC/SeqPurge).
                             Default value: ''
  -long_read                 Support long reads (> 1kb).
                             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'.
  --settings [file]          Settings override file (no other settings files are used).

MappingQC changelog

MappingQC 2024_08-110-g317f43b9

2023-11-08 Added long_read support.
2023-05-12 Added 'read_qc' parameter.
2022-05-25 Added new QC metrics to WGS mode.
2021-02-09 Added new QC metrics for uniformity of coverage (QC:2000057-QC:2000061).
2020-11-27 Added CRAM support.
2018-07-11 Added build switch for hg38 support.
2018-03-29 Removed '3exons' flag.
2016-12-20 Added support for spliced RNA reads (relevant e.g. for insert size)

back to ngs-bits