Post by michelnivard on Mar 28, 2019 9:37:53 GMT
When excluding SNPs using the flag "--exclude-region-bp" the log reports all other SNPs as excluded see line highliged in red below
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.92.0 beta2
* (C) 2010-2018, The University of Queensland
* Please report bugs to: Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started at 09:33:27 UTC on Thu Mar 28 2019.
Hostname: michel-HP-Z640-Workstation
Accepted options:
--bfile simulation_set
--exclude-region-bp 6 29000000 4300Kb
--make-bed
--out simulation_set_NoMHC
Reading PLINK FAM file from [simulation_set.fam].
40000 individuals to be included from [simulation_set.fam].
Reading PLINK BIM file from [simulation_set.bim].
1207680 SNPs to be included from [simulation_set.bim].
Extracting SNPs 4300kb away from the position [chr=6; bp=29000000] in either direction ...
1204951 SNPs are excludeed.
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.92.0 beta2
* (C) 2010-2018, The University of Queensland
* Please report bugs to: Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started at 09:33:27 UTC on Thu Mar 28 2019.
Hostname: michel-HP-Z640-Workstation
Accepted options:
--bfile simulation_set
--exclude-region-bp 6 29000000 4300Kb
--make-bed
--out simulation_set_NoMHC
Reading PLINK FAM file from [simulation_set.fam].
40000 individuals to be included from [simulation_set.fam].
Reading PLINK BIM file from [simulation_set.bim].
1207680 SNPs to be included from [simulation_set.bim].
Extracting SNPs 4300kb away from the position [chr=6; bp=29000000] in either direction ...
1204951 SNPs are excludeed.