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Revision as of 21:27, 1 December 2016
, 21:27, 1 December 2016→Full List of Options
| 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>
| <font face=Courier>'''--ChunkLengthMb 20.00'''</font>
| Minimac4 runs imputation on automated chunks. This parameters specifies the length of each chunk in Mbp.
| 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>
| <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.
| This parameters specifies the length of the buffer region to be analyzed on each side of the chunk (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>
| <font face=Courier>--states 200</font>
| <font face=Courier>--states 200</font>
| Maximum number of reference (or target) haplotypes to be examined during parameter optimization. By default = 200.
| Maximum number of reference (or target) haplotypes to be examined during parameter optimization. By default = 200.
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| <font face=Courier>'''--probThreshold 0.01'''</font>
| This parameter specifies the minimum posterior probability for a reference haplotype group to be included. If for some reason, the user believes that Minimac4 dropped the imputation accuracy significantly (compared to Minimac4), they should decrease the value to 0.0 (to be on the safe side). In general, reducing this value is not recommended as it will increase the compute time with no gain in accuracy
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| <font face=Courier>--help</font>
| <font face=Courier>--help</font>
| A short help on options.
| A short help on options
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| <font face=Courier>--lowMemory</font>
| <font face=Courier>'''--<s>lowMemory'''</s></font>
| If ON, a low memory version of Minimac3 will be run.
| This handles has been disabled in Minimac4
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| <font face=Courier>--cpus 5</font>
| <font face=Courier>--cpus 5</font>
