Allow use case AJRG

[richelbilderbeek]

This is what my group does.

• --ci 0.95: Add --ci 0.95 for assoc_qt with PLINK2 data #25
• Selecting SNPs, --snps rs16991615, added, extended at Let 'select_snps' work on 'assoc_qt_data' #41
• --maf 0.01
• --out /proj/nobackup/sens2017538/UKBB

Reading covariates works somewhat in plinkr, AFAIR the names are supplied with the .covar file:

 * [ ] `--covar /proj/nobackup/sens2017538/UKBB_41143_Ppiller/covar_200507.txt`
 * [ ] `--covar-name AGE_NORM AGE_NORM2 AGE_NORM3 AGE_NORM4 BMI array PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 SMOKE MENO OC HYSTER NRBIRTH TDI`

I can only guess what this does:

 * [ ] `--geno 0.05`

plinkr can do --glm (assoc_qt for PLINK2), but does not support the part after --glm

 * [ ] `--glm hide-covar cols=+a1freq,+ax`

Some easier ones:

 * [ ] `--hwe 1e-20`
 * [ ] `--keep /proj/sens2017538/nobackup/UKBB_IMP_DOSAGE_V3/IDs_to_indlude_NonRelCauc.ukb41143.20191202.txt`
 * [ ] `--keep-females`

File management using both PLINK binary and PLINK2 binary works. Here they use a mixed construct:

 * [x] `--pgen /proj/sens2017538/nobackup/UKBB_IMP_DOSAGE_V3_bim_bed/chr20.pgen`
 * [x] `--psam /proj/sens2017538/nobackup/UKBB_IMP_DOSAGE_V3/ukb41143.fam`
 * [x] `--pvar /proj/sens2017538/nobackup/UKBB_IMP_DOSAGE_V3_bim_bed/chr20.bim`

Reading phenotypes works in plinkr, yet these are supplied with the .phe file:

 * [x] `--pheno /proj/nobackup/sens2017538/UKBB_41143_Ppiller/phe_osteo_bmd.txt`
 * [x] `--pheno-name OC`