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

# 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