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SampleGender tool help

SampleGender (0.1-420-g3536bb0)

Determines the gender of a sample from the BAM file.

Mandatory parameters:
  -in <file>          Input BAM file.
  -method <enum>      Method selection: Read distribution on X and Y chromosome (xy), fraction of heterocygous variants on X chromosome (hetx), or coverage of SRY gene (sry).
                      Valid: 'xy,hetx,sry'

Optional parameters:
  -out <file>         Output file. If unset, writes to STDOUT.
                      Default value: ''
  -max_female <float> Maximum Y/X ratio for female (method xy).
                      Default value: '0.059999999999999998'
  -min_male <float>   Minimum Y/X ratio for male (method xy).
                      Default value: '0.089999999999999997'
  -min_female <float> Minimum heterocygous SNP fraction for female (method hetx).
                      Default value: '0.23999999999999999'
  -max_male <float>   Maximum heterocygous SNP fraction for male (method hetx).
                      Default value: '0.14999999999999999'
  -sry_cov <float>    Maximum average coverage of SRY gene for males (method sry).
                      Default value: '20'

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'.

SampleGender changelog

SampleGender 0.1-420-g3536bb0

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