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Revision as of 21:23, 1 December 2016
, 21:23, 1 December 2016no edit summary
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| <font face=Courier>'''--memUsage'''</font>
| <font face=Courier>'''--memUsage'''</font>
| If this handle is ON, Minimac4 will NOT run the imputation, but instead report an estimated memory usage summary. It will also report some minor instructions to change the memory usage by tweaking parameters in the command line. This summary might enable users to get an idea of memory consumption and modify it, if need be, before starting the imputation experiment. [Default: OFF]
| If this handle is ON, Minimac4 will NOT run the imputation, but instead report an estimated memory usage summary. It will also report some minor instructions on how to change the memory usage by tweaking parameters in the command line. This summary might enable users to get an idea of memory consumption and modify it, if need be, before starting the imputation experiment. [Default: OFF]
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| <font face=Courier>--chr 22</font>
| <font face=Courier>--chr 22</font>
| End position for imputation by chunking. Would not work without <font face=Courier>--chr</font> option.
| End position for imputation by chunking. Would not work without <font face=Courier>--chr</font> option.
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| <font face=Courier>--window 5000</font>
| Length of buffer region (in bp units) on either side of <font face=Courier>--start</font> and <font face=Courier>--end</font>. By default = 500000 (if chunking is done) and = 0 (if no chunking is being done).
| Length of buffer region (in bp units) on either side of <font face=Courier>--start</font> and <font face=Courier>--end</font>. By default = 500000 (if chunking is done) and = 0 (if no chunking is being done).
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| <font face=Courier>--ChunkLengthMb 20.00</font>
| Minimac4 runs imputation on automated chunks. This parameters specifies the length of each chunk in Mbp.
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| <font face=Courier>--ChunkOverlapMb 3.00</font>
| This parameters specifies the length of the buffer region on each side of the chunk specified above (in Mbp). Thus, if a user inputs <font face=Courier>--ChunkLengthMb 20.00</font> and <font face=Courier>--ChunkOverlapMb 3.00</font>, Minimac4 would analyze 26 Mbp chunks at a time.
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| <font face=Courier>--rec</font>
| <font face=Courier>--rec</font>
| Recombination File from previous run of Minimac/Minimac3. (<font face=Courier>--err</font> parameter must also be provided, if using this handle)
| Recombination File from previous run of Minimac/Minimac3. (<font face=Courier>--err</font> parameter must also be provided, if using this handle)
