RAREMETAL Change Log

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Change Log

  • For versions 4.15.0 and later, see the official "releases" page on GitHub: https://github.com/statgen/raremetal/releases
    • Note: versions in the 4.14.x series were prone to a bug with that gave incorrect results for SKAT and burden test methods.
    • Note: users of a specific long-lived pre-release v4.15.0 candidate ( April 19, 2018 ) may be affected by an issue with which variants are selected for analysis. If your version incorporates the linked GitHub commit, your results may be affected. Previous release candidates based on that branch should be ok.
  • Version 4.14.0 released (11/27/2016)
    • Optimized method for unbalanced studies with no family structure (--useExact). Check RAREMETAL METHOD
    • bug fixes in conditional analysis
    • fixed headers
    • more methods in burden test
  • Version 4.13.9 released (07/14/2016)
    • The source code has been optimized to prepare for incoming new meta-analysis method in next version.
    • Reduced running time when reading >10,000s individuals from vcf
    • Fixed seg fault in raremetalworker for calculating SNP HWE p value when sample size > 40k
    • A seg fault: sometimes you only have very few variants but raremetal still tries to calculate GC.
  • Version 4.13.8 released (12/13/2015)
    • when grouping from vcf, raremetal now obtains information only from "ANNOFULL" field.
    • fixed seg fault in matching --annotation option to vcf annotation.
    • with empty --annotation option, raremetal now groups all non-intergenic variants.
    • fixed a bug in conditional analysis when there are multiple variants to condition on.
    • fixed a seg fault in calculating genomic control.
    • add --variantList option in RaremetalWorker to only calculate variance-covariance matrix between certain markers.
    • add --range option in both Raremetal and RaremetalWorker to focus on given region only.
  • Version 4.13.7 released. (9/18/2015).
    • group file generated from annotated vcf is now stored in "test.groupfile" under current running directory.
    • use -O0 option in compiling. In very rare situations, gcc optimization will affect the results.
    • tabix RMW output with --zip toggled.
    • In SKAT meta analysis, skip the variant when all its lambdas are zero.
    • bug fixes in conditional analysis: in very rare situation raremetal takes rvtest input as raremetalworker input.
    • add --altMAF option to exclude studies in which a variant is not present.
  • Version 4.13.6 released. (3/8/2015)
    • add a new option --mergedVCFID to recognize VCF files with sample IDs in "FAMID_PID" format
    • add a new option --flagDosage to flag the field name to label dosage in VCF file.
  • Version 4.13.5 released. (9/29/2014)
    • a bug fixed in conditional analysis in raremetal.
  • Version 4.13.4 released.
    • store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.
  • Version 4.13.3 released.
    • read rvtest output format correctly in raremetal.
  • Version 4.13.2.
    • fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.
  • Version 4.13.1.
    • fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.
  • version 4.13
    • fixed bug when using --vcX option.
    • Fixed bug estimating kinshipX with female samples.
    • Added --kinOnly option for generating kinship only without association analysis.
    • Added --geneMap option to allow user input for gene-mapping file.
  • version 4.12.1
    • fixed command interface display issue in raremetalworker.
  • version 4.12
    • improved make file for better compilation.
  • version 4.11
    • fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).
  • version 4.10
    • fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).

Version 4.8 and before

  • Released version 0.4.7 (4/24/2014).
    • 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.
    • merged raremetal and raremetalworker in one package following version number of raremetalworker.
    • completed testing compiling on various platforms.
  • Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)
  • Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)
  • Released version 0.4.4. (3/17/2014)
    • bug fixed when alleles are flipped in group file.
    • fixed hwe=0.0 issue for monomorphic sites.
  • 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.
  • Released version 0.4.2. (3/10/2014)
    • fixed a bug that could possibly cause compiling error in some Linux system. male heterozygous
    • male genotypes on chromosome X are considered missing.
    • bug fixed for SKAT when there are two variants in a group
    • bug fixed in Makefile for easy compiling.
  • Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.
  • Released version 0.4.0.
    • added phone home function. Saved Recessive and dominant results in separate files.
    • a few bugs fixed to properly handling missing genotypes.
    • Major change in command options.
    • allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.
  • Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)
  • Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)
  • Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)
  • Version 0.3.1 released to fix a bug when one of the alleles coded as missing.
  • Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)
  • Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)
  • Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)
  • Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)
  • 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)
  • Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)
  • Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)
  • Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)
  • Version 0.0.1 released. (2/24/2013)
  • Version 0.0.1 released to U of M CSG group. (2/13/2013)
  • Fixed a bug when there is missing genotype from VCF file. (2/2013)
  • Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)
  • Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)
  • Updated output format for monomorphic sites. (12/7/2012)
  • Version 0.0.6 released. (12/6/2012)
  • Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)
  • Version 0.0.4 released. (12/5/2012)
  • More messages coded into log file. (12/4/2012)
  • Updated output format. Version 0.0.3 released. (12/3/2012)
  • Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)
  • Added HWE pvalue and call rate in summary statistics output. (11/27/2012)
  • 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)
  • Enabled writing log file by defalut. (11/18/2012)
  • Uploaded to public wiki. (11/16/2012)
  • Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)
  • Version 0.0.1 was released on 11/13/2012.