RAREMETAL Change Log

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Change Log

  • 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.