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| | [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL and RAREMETALWORKER Tutorial'''] | | [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL and RAREMETALWORKER Tutorial'''] |
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| − | == Change Log ==
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| − | * Version 0.0.1 was released on 11/13/2012.
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| − | * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)
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| − | * Uploaded to public wiki. (11/16/2012)
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| − | * Enabled writing log file by defalut. (11/18/2012)
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| − | * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)
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| − | * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)
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| − | * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)
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| − | * Updated output format. Version 0.0.3 released. (12/3/2012)
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| − | * More messages coded into log file. (12/4/2012)
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| − | * Version 0.0.4 released. (12/5/2012)
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| − | * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)
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| − | * Version 0.0.6 released. (12/6/2012)
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| − | * Updated output format for monomorphic sites. (12/7/2012)
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| − | * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)
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| − | * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)
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| − | * Fixed a bug when there is missing genotype from VCF file. (2/2013)
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| − | * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)
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| − | * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)
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| − | * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)
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| − | * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)
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| − | * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)
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| − | * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)
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| − | * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)
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| − | * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)
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| − | * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)
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| − | * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.
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| − | * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.
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| − | * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)
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| − | * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.
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| − | * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)
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| − | * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)
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| − | * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)
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| − | * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)
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