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TrioMaternalContamination tool help

TrioMaternalContamination (2021_12-80-g5ff26d8f)

Detects maternal contamination of a child using SNPs from parents.

Determines the percentage of heterozygous SNPs passed on to the child from mother/father.
This percentage should be similar for mother/father. If it is not, maternal contamination is likely.

Mandatory parameters:
  -bam_m <file>        Input BAM/CRAM file of mother.
  -bam_f <file>        Input BAM/CRAM file of father.
  -bam_c <file>        Input BAM/CRAM file of child.

Optional parameters:
  -min_depth <int>     Minimum depth for calling SNPs.
                       Default value: '3'
  -min_alt_count <int> Minimum number of alternate observations for calling a SNP.
                       Default value: '1'
  -build <enum>        Genome build used to generate the input.
                       Default value: 'hg38'
                       Valid: 'hg19,hg38'
  -out <file>          Output file. If unset, writes to STDOUT.
                       Default value: ''
  -ref <file>          Reference genome for CRAM support (mandatory if CRAM is used).
                       Default value: ''

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'.

TrioMaternalContamination changelog

TrioMaternalContamination 2021_12-80-g5ff26d8f

2020-11-27 Added CRAM support.
2020-06-18 Initial version of the tool.

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