Plink with hwe option does not work

Question

[east_chenyutang]

Hi all,

I am new to Plink, I was trying to extract SNPs based on base position with filters like maf and hwe, below are my Plink codes:

/home/Software/plink \
--bfile mydata \
--chr 1 --from-bp 10 --to-bp 100000 \
--hwe 1e-6 \
--make-bed \
--maf 0.01 \
--out OutputFile

When I only include maf option, the codes work fine, but when I have both maf and hwe options, the codes does not work. Could anyone see the possible problem there? Could the incompatibility between options be a possible reason? Maybe --chr cannot be used with --hwe or --bfile cannot be used with --hwe? I have no clue. Please help me. Lots of thanks in advance. By the way, the log file returned by Plink says "double free or corruption", does that mean something?

Best wishes,
Yutang

[Sam]

What do you mean by do not work? Do you have the output log?

[east_chenyutang]

Sorry for my vague description. I have and only have the output log, no other output files (bed, bim, fam) returned.

[chrchang523]

Please post the full .log file (or console output) from your failing run.

Answer 1

[Tao]

There is incompatibility between options in PLINK.

I would suggest you to separate your process into two steps: --hwe, --maf are for quality control; and --chr --from-bp --to-bp are for extracting.

And --out should be prefix names of output plink files, not folder name.

[east_chenyutang]

Thank you very much for your suggestion! I will give it a try. Also thanks for pointing out the mistake in --out option, I have changed the folder name to a file name in my post.

[Tao]

NO worries. Please upvote or accept my post if you think useful :)