SampleGender.md

SampleGender tool help

SampleGender (2025_07-127-g60fc6b39)

Determines the gender of a sample from the BAM/CRAM file.

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

Optional parameters:
  -out <file>         Output TSV file - one line per input BAM/CRAM file. If unset, writes to STDOUT.
                      Default value: ''
  -max_female <float> Maximum Y/X ratio for female (method xy).
                      Default value: '0.06'
  -min_male <float>   Minimum Y/X ratio for male (method xy).
                      Default value: '0.09'
  -min_female <float> Minimum heterozygous SNP fraction for female (method hetx).
                      Default value: '0.25'
  -max_male <float>   Maximum heterozygous SNP fraction for male (method hetx).
                      Default value: '0.05'
  -sry_cov <float>    Minimum average coverage of SRY gene for males (method sry).
                      Default value: '20'
  -build <enum>       Genome build used to generate the input (methods hetx and sry).
                      Default value: 'hg38'
                      Valid: 'hg19,hg38'
  -ref <file>         Reference genome for CRAM support (mandatory if CRAM is used).
                      Default value: ''
  -long_read          Support long reads (> 1kb) and uses single-end reads for gender calculation.
                      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).

SampleGender changelog

SampleGender 2025_07-127-g60fc6b39

2024-02-29 Added parameter to include single-end reads (long-read).
2022-08-05 Ignoring duplicate, secondary and supplementary alignments in methods 'xy' and 'sry' now.
2020-11-27 Added CRAM support.
2018-07-13 Change of output to TSV format for batch support.
2018-07-11 Added build switch for hg38 support.

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