Is there a way to tell PLINK and VCFtools to sort the samples in a particular order?

Question

[beausoleilmo]

I wonder if it's possible to output the samples names in a particular order in a VCF file and in a PLINK output (BED or PED).

I have a vector on with I'd like to sort:

 samples = c("JP3048_for", "JP3162_for", "JP3171_for", "JP3402_for", "JP343_for", 
"JP3539_for", "JP3574_for", "JP3582_for", "JP3631_for", "JP3633_for", 
"JP3636_for", "JP3640_for", "JP3642_for", "JP3652_for", "JP3657_for", 
"JP3658_for", "JP3661_for", "JP3670_for", "JP3676_for", "JP3681_for", 
"JP3683_for", "JP3687_for", "JP3695_for", "JP3697_for", "JP3738_for", 
"JP3747_for", "JP3748_for", "JP3750_for", "JP3751_for", "JP3752_for", 
"JP3753_for", "JP3754_for", "JP3755_for", "JP3774_for", "JP3790_for", 
"JP3835_for", "JP3839_for", "JP3844_for", "JP3894_for", "JP3895_for", 
"JP3913_for", "JP3914_for", "JP3922_for", "JP3923_for", "JP3924_for", 
"JP3934_for", "JP3943_for", "JP3959_for", "JP3960_for", "JP687_for", 
"SH241_for", "SH367_for", "SH520_for", "SH824_for", "SH851_for", 
"SH855_for", "JP261_ful", "JP262_ful", "JP278_ful", "JP286_ful", 
"JP290_ful", "JP293_ful", "JP294_ful", "JP295_ful", "JP303_ful", 
"JP306_ful", "JP309_ful", "JP342_ful", "JP348_ful", "JP359_ful", 
"JP393_ful", "JP411_ful", "JP475_ful", "JP506_ful", "JP512_ful", 
"JP3607_mag", "JP3626_mag", "JP3656_mag", "JP3665_mag", "JP3666_mag", 
"JP3684_mag", "JP3688_mag", "JP3690_mag", "JP3693_mag", "JP3699_mag", 
"JP3740_mag", "JP3746_mag", "JP3810_mag", "JP3565_sca", "JP3583_sca", 
"JP3587_sca", "JP3610_sca", "JP3647_sca", "JP3653_sca", "JP3655_sca", 
"JP3664_sca")

Is there a way to output a bed or a ped with a particular output order?

Answer 1

[chrchang523]

PLINK 1.9's --indiv-sort flag (https://www.cog-genomics.org/plink2/data#indiv_sort ) lets you do this. (If you want to export a VCF, though, you'll need to run PLINK twice, once with --indiv-sort + --make-bed, and then once with --recode vcf using the newly sorted fileset.)