From now on, I will try to archive our update log here.

2020-08-05 (v2.3.3)

  • Thanks to report from @charlisech, we were able to pinpoint a bug related to sample selection when using bgen data.

2020-07-15 (v2.3.2)

  • Fix off by one error in PRSet best score output
  • Fix problem for bgen file when sample selection is performed on bgen files containing sample information

2020-05-30 (v2.3.1.e)

  • Fix bug where SNPs without missingness will be wrongly considered as having 100% missingness
  • Fix error log where PRSice should now correct stat if a parameter is missing the required arguments

2020-05-29 (v2.3.1.d)

  • Fix segmentation fault when --ld is used

2020-05-28 (v2.3.1.c)

  • Fix problem with missing covariate
  • Fix Rscript such that it properly read in phenotype file when --pheno-co l is specified

2020-05-26 (v2.3.1.b)

  • Fix best score output when --ignore-fid is used
  • Also fix Rscript covariate and phenotype file read when handling IDs star t with 00 and when --ignore-fid is used

2020-05-26 (v2.3.1.a)

  • Fix bar plot with covariate. Was plotting the full R2 instead of the PRS.R2

2020-05-23 (v2.3.1)

  • Update Rscript such that it match features in executable (thus avoid problem in plotting)
  • Fix a bug where PRSice will crash when there are missing covariates

2020-05-21 (v2.3.0.e)

  • Fix Rscript bar plot problem

2020-05-21 (v2.3.0.d)

  • Fix problem introduced by previous fix.
  • Was hoping 2.3.0's unit test will help reducing the amount of bugs. Sorry for the troubles.

2020-05-20 (v2.3.0.c)

  • Fix all score output format
  • Fix problem with --no-regress. Might still have problem with --no-regress --score con-std

2020-05-19 (v2.3.0.b)

  • Fix error where sample selection will distort phenotype loading, loading the wrong phenotype to wrong sample. As this is a major bug, we deleted the previous 2 releases. Sorry for the troubles.

2020-05-19 (v2.3.0.a)

  • Fix output error where we always say 0 valid phenotype were included for continuous trait
  • Fix problem with permutation where PRSice will crash if input are rank deficient
  • Fix problem when provide a binary phenotype file with a fam file containing -9 as phenotype, PRSice will wrongly state that there are no phenotype presented
  • Fix problem in Rscript where if sample ID is numeric and starts with 0, the best file will not merge with the phenotype file, causing 0 valid PRS to be observed

2020-05-18 (v2.3.0)

  • We now support multi-threaded clumping (separated by chromosome)
  • Genotypes will be stored to memory during clumping (increase memory usage, significantly speed up clumping)
  • Will only generate one .prsice file for all phenotypes
    • .prsice file now has additional column call "Pheno"
  • Introduced --chr-id which generate rs id based on user provided formula (see detail for more info)
  • Format of --base-maf and --base-info are now changed to <name>:<value> from <name>,<value>
  • Fix a bug related to ambiguous allele dosage flipping when --keep-ambig is used
  • Better mismatch handling. For example, if your base file only provide the effective allele A without the non-effective allele information, PRSice will now do dosage flipping if your target file has G/C as effective allele and A /T as an non-effective allele (whereas previous this SNP will be considered as a mismatch)
  • Fix bug in 2.2.13 where PRSice won't output the error message during command parsing stage
  • If user provided the --stat information, PRSice will now error out instead of trying to look for BETA or OR in the file.
  • PRSice should now better recognize if phenotype file contains a header
  • various small bug fix