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SampleAncestry tool help

SampleAncestry (2022_12-82-g025eb99e)

Estimates the ancestry of a sample based on variants.

Mandatory parameters:
  -in <filelist>        Input variant list(s) in VCF or VCF.GZ format.

Optional parameters:
  -out <file>           Output TSV file. If unset, writes to STDOUT.
                        Default value: ''
  -min_snps <int>       Minimum number of informative SNPs for population determination. If less SNPs are found, 'NOT_ENOUGH_SNPS' is returned.
                        Default value: '1000'
  -score_cutoff <float> Absolute score cutoff above which a sample is assigned to a population.
                        Default value: '0.32'
  -mad_dist <float>     Maximum number of median average diviations that are allowed from median population score.
                        Default value: '4.2'
  -build <enum>         Genome build used to generate the input.
                        Default value: 'hg38'
                        Valid: 'hg19,hg38'

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'.

SampleAncestry changelog

SampleAncestry 2022_12-82-g025eb99e

2021-05-17 Population assignment is based on abolute score and on median/mad now. Should be much more accurate now especially for admixed samples.
2020-08-07 VCF files only as input format for variant list.
2018-12-10 Fixed bug in handling of 'pop_dist' parameter.
2018-07-11 Added build switch for hg38 support.
2018-07-03 First version.

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