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SampleGender.md

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SampleGender tool help

SampleGender (2024_08-110-g317f43b9)

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: ''
  -include_single_end_reads  In bam mode: include reads which are not (properly) paired. Required e.g. for long-read input data.
                             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 2024_08-110-g317f43b9

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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