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VcfCalculatePRS tool help

VcfCalculatePRS (2024_08-113-g94a3b440)

Calculates the Polgenic Risk Score(s) for a sample.

The PRS VCF files have to contain WEIGHT and POP_AF fields in the INFO column.
Additionally some information about the PRS score is required in the VCF header.
An example VCF file can be found at https://github.com/imgag/ngs-bits/blob/master/src/tools-TEST/data_in/VcfCalculatePRS_prs2.vcf

Mandatory parameters:
  -in <file>        Tabix indexed VCF.GZ file of a sample.
  -prs <filelist>   List of PRS VCFs.
  -bam <file>       BAM file corresponding to the VCF.
  -out <file>       Output TSV file containing Scores and PRS details

Optional parameters:
  -details <file>   Output TSV containing each variant with weight, allele count and population AF.
                    Default value: ''
  -ref <file>       Reference genome FASTA file. If unset, 'reference_genome' from the 'settings.ini' file is used.
                    Default value: ''
  -min_depth <int>  Depth cutoff below which uncalled SNPs are considered not callable and POP_AF is used instead of genotype.
                    Default value: '10'

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).

VcfCalculatePRS changelog

VcfCalculatePRS 2024_08-113-g94a3b440

2024-06-05 Added support for imputed variants.
2024-04-22 Added output of factors and support for wt variants.
2022-12-15 Added BAM depth check and population AF.
2020-07-22 Initial version of this tool.

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