PLINK 1.9 --split-x b37

[Sander W. van der Laan]

Hi,

I have three datasets. 

First some background. 

I executed the QC, and check the sex. For the latter I first filtered my data to include only high-quality genotypes to determine sex using --check-sex. I removed the erroneous samples. Also, the chromosomes are split, in the original (raw) binary PLINK data - so --split-x b37 errors out.

Can I assume that the 'splitting' is correct? Or should I do --merge-x and next split-x b37 to make sure everything is in the right genomic order/place? 

Am thinking that perhaps some SNPs may be wrongfully on XY or vice versa

Thanks,

Sander

[Chris Chang]

If you suspect the original splitting may have involved the wrong reference genome build, yes, you can use --merge-x followed by an appropriate --split- command.  (Note that PLINK2 --split-par is more ergonomic than PLINK 1.9 --split-x, since --split-par does not change variant order.)

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[Sander W. van der Laan]

Yes, I did this. I didn’t do the original splitting. It was merely based on the genotype-calling software which of course is using the annotation file and whatever chr-bp combination is in there. It does produce a binary PLINK file, but apparently the order of things isn’t right. 

So, first I merged everything using plink19. Next, I applied plink2 and the --split-par option. Now everything made sense again.

Thanks!

Sander