Reorder filter options in PLINK

Question

[panacotaforcota]

Dear All,

I try to make QC steps in PLINK, but I faced problem with order of steps. For example, I want such order:

  --bfile ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes
  --geno <>
  --maf <>
  --hwe <>
  --make-bed
  --out ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.qc1

but PLINK executes the request only in that order:

  --geno <>
  --hwe <>
  --maf <>

How can I control order of filter options? I don't want do it separately, because it requires a lot of time to rewrite files every new step.

[chrchang523]

1. Are you aware that the final result is identical regardless of the order you execute these three filters in? Order only matters if you have both sample- and variant-filtering flags.
2. If —bfile/—make-bed is taking longer than you’d like, try plink 2.0 —pfile/—make-pgen.

[panacotaforcota]

Plink2 doesn't have --check-sex. Why?

[chrchang523]

Plink2 is under development, and —check-sex is lower priority than many other commands since you can just export a chrX+chrY .bed file and run plink 1.9.