Specify .bed, .bim, .fam separately

[choishingwan]

Specify .bed, .bim, .fam separately

[choishingwan]

This is now implemented in 52de5cf and will be included in the next release.

To use this function, simply do:
--target <bfile Prefix>,<fam file>

Note: No space

[JoniColeman]

This doesn't work in the current build (see output below):

PRSice 2.0.10.beta (26 September 2017)
https://github.com/choishingwan/PRSice
(C) 2016-2017 Jack Euesden, Cathryn M. Lewis, Paul F. O'Reilly, Sam Choi
GNU General Public License v3

Thu Sep 28 09:41:24 2017

/mnt/lustre/groups/ukbiobank/usr/KCL_Data_Analyses/PRSice \
    --base [path to base file] \
    --target /mnt/lustre/datasets/ukbiobank/June2017/Genotypes/ukb_binary_v2,/mnt/lustre/groups/ukbiobank/KCL_Data/Genotypes/ukb1657_cal_chr1_v2_s488374.fam \
    --type bed \
    --binary-target F \
    --out [redacted]\
    --thread 4 \
    --keep [path]/Keeps_For_PRSice.txt \
    --bar-levels 0.05,1 \
    --pheno-file [path]Pheno.txt \
    --clump-kb 250 \
    --clump-p 1 \
    --clump-r2 0.1 \
    --extract [path]_Includes.txt \
    --stat BETA \
    --chr CHR \
    --A1 A1 \
    --A2 A2 \
    --snp SNP \
    --bp BP \
    --se SE \
    --pvalue P \
    --beta \
    --fastscore

Loading Genotype file: /mnt/lustre/datasets/ukbiobank/June2017/Genotypes/ukb_binary_v2 (bed)
With external fam file: /mnt/lustre/groups/ukbiobank/KCL_Data/Genotypes/ukb1657_cal_chr1_v2_s488374.fam
terminate called after throwing an instance of 'std::runtime_error'
  what():  Error: Cannot open bim file: /mnt/lustre/datasets/ukbiobank/June2017/Genotypes/ukb_binary_v2,/mnt/lustre/groups/ukbiobank/KCL_Data/Genotypes/ukb1657_cal_chr1_v2_s488374.fam.bim

This can be worked around by creating a symbolic link to the different components with a shared prefix

[choishingwan]

The update b22610e has now solve this problem. In addition, that should no longer complain about size of bed file when sex chromosome stuff is included (Haven't got an example file for me to test that though...)