Command-Line Options

Option	Type	Required	Description
--enable-imputation	NA	Yes	Set to true to enable vcf imputation pipeline
--imputation-ref-panel-dir	STRING	Yes	Directory containing per-chromosome reference panel VCF
--imputation-ref-panel-prefix	STRING	Yes	Prefix for reference panel files
--imputation-genome-map-dir	STRING	Yes	Directory containing per-chromosome genome map files
--imputation-chunk-input-region	STRING	Yes for single region	Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). For chrX, treat PAR and non-PAR regions as different chromosome in order to avoid mixing ploidy.
--imputation-chunk-input-region-list	STRING	Yes for list of regions	Text file listing chromosomes or regions to be processed, one chromosome/region per line
--imputation-phase-input-list	STRING	Yes for multiple VCF files	Text file listing sample input in VCF/BCF format, one input file per line
--output-directory	STRING	Yes	Output directory
--output-file-prefix	STRING	Yes	Output files prefix
--imputation-phase-threads	INT	No	Specify the number of threads to use. Default is the number of system thread
--imputation-phase-filter-input-sample-in-ref	NA	No	Default is true: if sample ID matches between reference panel and sample input, then the corresponding samples are ignored from the reference panel to avoid imputation against itself. To be turned to false if all samples from the reference panel should be kept regardless of their presence in the sample input.
--impute-reference-only-variants	STRING	No	Default is false. If set to true, allows imputation at variants only present in the reference panel. The use of this option is intended only to allow imputation at sporadic missing variants. If the number of missing variants is non-sporadic, please re-run the genotype likelihood computation at all reference variants and avoid using this option, since data from the reads should be used.

--enable-imputation

NA

Yes

Set to true to enable vcf imputation pipeline

--imputation-ref-panel-dir

STRING

Yes

Directory containing per-chromosome reference panel VCF

--imputation-ref-panel-prefix

STRING

Yes

Prefix for reference panel files

--imputation-genome-map-dir

STRING

Yes

Directory containing per-chromosome genome map files

--imputation-chunk-input-region

STRING

Yes for single region

Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). For chrX, treat PAR and non-PAR regions as different chromosome in order to avoid mixing ploidy.

--imputation-chunk-input-region-list

STRING

Yes for list of regions

Text file listing chromosomes or regions to be processed, one chromosome/region per line

--imputation-phase-input-list

STRING

Yes for multiple VCF files

Text file listing sample input in VCF/BCF format, one input file per line

--output-directory

STRING

Yes

Output directory

--output-file-prefix

STRING

Yes

Output files prefix

--imputation-phase-threads

INT

No

Specify the number of threads to use. Default is the number of system thread

--imputation-phase-filter-input-sample-in-ref

NA

No

Default is true: if sample ID matches between reference panel and sample input, then the corresponding samples are ignored from the reference panel to avoid imputation against itself. To be turned to false if all samples from the reference panel should be kept regardless of their presence in the sample input.

--impute-reference-only-variants

STRING

No

Default is false. If set to true, allows imputation at variants only present in the reference panel. The use of this option is intended only to allow imputation at sporadic missing variants. If the number of missing variants is non-sporadic, please re-run the genotype likelihood computation at all reference variants and avoid using this option, since data from the reads should be used.