Difference between revisions of "Minimac3 ChangeLog"
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Date : February 27, 2015 | Date : February 27, 2015 | ||
| − | Add parameter --log which will output a log file (BUT not print | + | Add parameter --log which will output a log file (BUT not print on the screen). Also added legacy parameter --myChromosome which will enable users to use special chromosomes (apart from 1-22 and X) |
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==Ver 1.0.9 (February 20, 2015)== | ==Ver 1.0.9 (February 20, 2015)== | ||
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Date : February 20, 2015 | Date : February 20, 2015 | ||
| − | Removed dependcies on boost directory. Converted all double to | + | Removed dependcies on boost directory. Converted all double to float. Had to change the main imputation formula to work well for large values. Also updated Rsq calulation formual to avoid underflow as a result of using float. Made minor changes to memory allocation so as to remove all 2-d or 3-d look-ups. Updated a loop to remove repeat allocation, similar to minimac2. Now it is faster and uses much lesser memory. |
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==Ver 1.0.7 (January 31, 2015)== | ==Ver 1.0.7 (January 31, 2015)== | ||
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Date : October 3, 2014 | Date : October 3, 2014 | ||
| − | Implemented chromosome X imputation (both PAR and non-PAR). Also | + | Implemented chromosome X imputation (both PAR and non-PAR). Also added bgzip option to enable tabix options. |
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==Ver 1.0.4 (September 19, 2014)== | ==Ver 1.0.4 (September 19, 2014)== | ||
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Date : September 19, 2014 | Date : September 19, 2014 | ||
| − | Improved the chuking option for the compressed files. Updated name | + | Improved the chuking option for the compressed files. Updated name OPTM to M3VCF (Minimac3 VCF). Changed handle to --processReference. Added the option to add parameter estimates within M3VCF files which can be used for later runs. Added a new handle --updateModel that will allow users to update these estimates using the target panel as well, if and when they think necessary. |
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==Ver 1.0.2 (August 28, 2014)== | ==Ver 1.0.2 (August 28, 2014)== | ||
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Date : August 28, 2014 | Date : August 28, 2014 | ||
| − | Mended a bug related to --vcfoutput option when used with --gzip | + | Mended a bug related to --vcfoutput option when used with --gzip option. Also added a option --format to manage handles in the FORMAT field for output VCF files. |
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==Ver 1.0.1 (August 6, 2014)== | ==Ver 1.0.1 (August 6, 2014)== | ||
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Date : August 6, 2014 | Date : August 6, 2014 | ||
| − | Added the --window option that will allow a buffer region around | + | Added the --window option that will allow a buffer region around chunks. Also implemented this --start, --end and --window option on OPTM files. Minimac3 will, thus, be able to handle chunks on OPTM files as well. However, it will not perform the optimal allocation again but just extract the chunk from the given file. |
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==Ver 1.0.0 (July 21, 2014)== | ==Ver 1.0.0 (July 21, 2014)== | ||
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Date : July 21, 2014 | Date : July 21, 2014 | ||
| − | Added the --vcfOutput option that will output the dosage in VCF | + | Added the --vcfOutput option that will output the dosage in VCF format as well. Improved it by allowing to flush out VCF file after every 200 samples to save memory. Also implemented openmp to allow parallel computing. |
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==Ver 0.7.1 (June 8, 2014)== | ==Ver 0.7.1 (June 8, 2014)== | ||
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Date : June 8, 2014 | Date : June 8, 2014 | ||
| − | Added the --golden option that can calculate the actual R-square | + | Added the --golden option that can calculate the actual R-square if the true/hard genotypes are provided in a vcf file. Made minor editions for debugging. |
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==Ver 0.6.2 (June 8, 2014)== | ==Ver 0.6.2 (June 8, 2014)== | ||
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Date : June 8, 2014 | Date : June 8, 2014 | ||
| − | Edited bug in VCF packing part that was giving slightly less | + | Edited bug in VCF packing part that was giving slightly less optimized configurations. |
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==Ver 0.6.1 (June 7, 2014)== | ==Ver 0.6.1 (June 7, 2014)== | ||
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Date : June 7, 2014 | Date : June 7, 2014 | ||
| − | Worked on an important bug that gave memory overflow in large | + | Worked on an important bug that gave memory overflow in large samples. Name changed to Minimac3. Added utility for VCF output format that would enable users to easy data manipulation. |
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==Ver 0.5.1 (April 9, 2014)== | ==Ver 0.5.1 (April 9, 2014)== | ||
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Date : April 9, 2014 | Date : April 9, 2014 | ||
| − | Removed futher bugs. Modified to use lesser memory and run faster. | + | Removed futher bugs. Modified to use lesser memory and run faster. The Unique.cpp file was updated according to Goncalo's packVcf software. Target Data is being read more effeciently. Scaffolding done locally during imputation. Changed name to Minimac2. |
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==Ver 0.4.1 (March 14, 2014)== | ==Ver 0.4.1 (March 14, 2014)== | ||
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Date : March 14 2014 | Date : March 14 2014 | ||
| − | Removed bug with --sample. Added lots of other options like --chr, | + | Removed bug with --sample. Added lots of other options like --chr,--start, --end, --rounds, --states etc. Added data structure for variant type. Added structure so as NOT to use haplotype data after reading it once. Now the code uses the reduced haplotype structure once it has read the data. This was uses lesser memory. |
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==Ver 0.2.1 (January 29, 2014)== | ==Ver 0.2.1 (January 29, 2014)== | ||
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Date : January 29 2014 | Date : January 29 2014 | ||
| − | Improved on the speed in parameter estimation part by NOT | + | Improved on the speed in parameter estimation part by NOT calculating the optimal allocation everytime, instead update it from the original allocation. Updated to use --refSnps for reference, use --vcfTarget for target files. |
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==Ver 0.1.1 (May 25, 2014)== | ==Ver 0.1.1 (May 25, 2014)== | ||
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Date : May 25 2013 | Date : May 25 2013 | ||
| − | Started working on the basis of code of minimac. Implemented State | + | Started working on the basis of code of minimac. Implemented State Space Reduction Method for HMM calculations. Implemented the Parameter Estimation part and Optimal Allocation part. |
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Revision as of 03:50, 27 February 2015
Introduction
Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes (say from MaCH) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
This wiki page gives users a summary of changes over the versions.
Change Log Summary
This section gives details of the changes over the different versions.
Minimac3 Changes:
Ver 1.0.10 (February 27, 2015)
Version : 1.0.10 Author : Sayantan Das Date : February 27, 2015
Add parameter --log which will output a log file (BUT not print on the screen). Also added legacy parameter --myChromosome which will enable users to use special chromosomes (apart from 1-22 and X)
Ver 1.0.9 (February 20, 2015)
Version : 1.0.8, 1.0.9 Author : Sayantan Das Date : February 20, 2015
Removed dependcies on boost directory. Converted all double to float. Had to change the main imputation formula to work well for large values. Also updated Rsq calulation formual to avoid underflow as a result of using float. Made minor changes to memory allocation so as to remove all 2-d or 3-d look-ups. Updated a loop to remove repeat allocation, similar to minimac2. Now it is faster and uses much lesser memory.
Ver 1.0.7 (January 31, 2015)
Version : 1.0.7 Author : Sayantan Das Date : January 31, 2015
Fixed minor bugs and made thigsn ready for final release !!!
Ver 1.0.6 (November 4, 2014)
Version : 1.0.6 Author : Sayantan Das Date : November 4, 2014
Mended some minor bugs.
Ver 1.0.5 (October 4, 2014)
Version : 1.0.5 Author : Sayantan Das Date : October 3, 2014
Implemented chromosome X imputation (both PAR and non-PAR). Also added bgzip option to enable tabix options.
Ver 1.0.4 (September 19, 2014)
Version : 1.0.4 Author : Sayantan Das Date : September 19, 2014
Improved the chuking option for the compressed files. Updated name OPTM to M3VCF (Minimac3 VCF). Changed handle to --processReference. Added the option to add parameter estimates within M3VCF files which can be used for later runs. Added a new handle --updateModel that will allow users to update these estimates using the target panel as well, if and when they think necessary.
Ver 1.0.2 (August 28, 2014)
Version : 1.0.2 Author : Sayantan Das Date : August 28, 2014
Mended a bug related to --vcfoutput option when used with --gzip option. Also added a option --format to manage handles in the FORMAT field for output VCF files.
Ver 1.0.1 (August 6, 2014)
Version : 1.0.1 Author : Sayantan Das Date : August 6, 2014
Added the --window option that will allow a buffer region around chunks. Also implemented this --start, --end and --window option on OPTM files. Minimac3 will, thus, be able to handle chunks on OPTM files as well. However, it will not perform the optimal allocation again but just extract the chunk from the given file.
Ver 1.0.0 (July 21, 2014)
Version : 1.0.0 Author : Sayantan Das Date : July 21, 2014
Added the --vcfOutput option that will output the dosage in VCF format as well. Improved it by allowing to flush out VCF file after every 200 samples to save memory. Also implemented openmp to allow parallel computing.
Ver 0.7.1 (June 8, 2014)
Version : 0.7.1 Author : Sayantan Das Date : June 8, 2014
Added the --golden option that can calculate the actual R-square if the true/hard genotypes are provided in a vcf file. Made minor editions for debugging.
Ver 0.6.2 (June 8, 2014)
Version : 0.6.2 Author : Sayantan Das Date : June 8, 2014
Edited bug in VCF packing part that was giving slightly less optimized configurations.
Ver 0.6.1 (June 7, 2014)
Version : 0.6.1 Author : Sayantan Das Date : June 7, 2014
Worked on an important bug that gave memory overflow in large samples. Name changed to Minimac3. Added utility for VCF output format that would enable users to easy data manipulation.
Ver 0.5.1 (April 9, 2014)
Version : 0.5.1 Author : Sayantan Das Date : April 9, 2014
Removed futher bugs. Modified to use lesser memory and run faster. The Unique.cpp file was updated according to Goncalo's packVcf software. Target Data is being read more effeciently. Scaffolding done locally during imputation. Changed name to Minimac2.
Ver 0.4.1 (March 14, 2014)
Version : 0.4.1 Author : Sayantan Das Date : March 14 2014
Removed bug with --sample. Added lots of other options like --chr,--start, --end, --rounds, --states etc. Added data structure for variant type. Added structure so as NOT to use haplotype data after reading it once. Now the code uses the reduced haplotype structure once it has read the data. This was uses lesser memory.
Ver 0.2.1 (January 29, 2014)
Version : 0.2.1 Author : Sayantan Das Date : January 29 2014
Improved on the speed in parameter estimation part by NOT calculating the optimal allocation everytime, instead update it from the original allocation. Updated to use --refSnps for reference, use --vcfTarget for target files.
Ver 0.1.1 (May 25, 2014)
Version : 0.1.1 Author : Sayantan Das Date : May 25 2013
Started working on the basis of code of minimac. Implemented State Space Reduction Method for HMM calculations. Implemented the Parameter Estimation part and Optimal Allocation part.
Download
Minimac3 is available as an undocumented release version. The source files (and binary executable) are available for download in Source Files and commonly used reference panels in VCF and M3VCF formats are available for download in Reference Panels.
Useful Wiki Pages
There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:
- Minimac3 Imputation Cookbook (Recommended for New Users!!)
Contact
In case of any queries and bugs please contact Sayantan Das.
