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Revision as of 21:14, 1 December 2016
, 21:14, 1 December 2016no edit summary
| <font face=Courier>--nobgzip</font>
| <font face=Courier>--nobgzip</font>
| If ON, output files will be NOT bgzipped.
| If ON, output files will be NOT bgzipped.
|-
| <font face=Courier>--vcfBuffer 200</font>
| This is number of samples to be stored in the memory before writing a VCF file piece
|-
|-
| <font face=Courier>--vcfOutput</font>
| <font face=Courier>--vcfOutput</font>
|-
|-
| <font face=Courier>--format</font>
| <font face=Courier>--format</font>
| Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <font face=Courier>GT,DS,GP </font>[Default: <font face=Courier>GT,DS</font>]
| Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <font face=Courier>GT,DS,GP,HDS </font>. <font face=Courier>GT</font> stands for Genotype, <font face=Courier>DS</font> stands for genotype dosage, <font face=Courier>HDS</font> stands for haplotype dosage and <font face=Courier>GP</font> stands for genotype probabilities [Default: <font face=Courier>GT,DS</font>]
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|-
| <font face=Courier>--allTypedSites</font>
| <font face=Courier>--allTypedSites</font>
