Question: Plink : how to filter outliers for GWAS ?
0
gravatar for nlehmann
3.6 years ago by
nlehmann90
France
nlehmann90 wrote:

Hi, I'm new with GWAS studies and Plink. I have a set of 4 chromosomes, and more than 3000 individuals and nearly 200 000 SNP. I have already cleaned the data using this command (for each chromosome) :

plink --file chr5 --make-bed --out chr5 --geno 0.05 --maf 0.05 --mind 0.025 --hwe 0.001

Now my first question is is this relevant to do an PCA to select outliers even after using HWE ? And second question : the outputs of the command for each chromosome gives me different number of individuals. So we have something like :

# chr 2
52627 variants and 3027 people pass filters and QC.
# chr 5
41022 variants and 3032 people pass filters and QC.
# chr 13
24171 variants and 3004 people pass filters and QC.
# chr 16
19664 variants and 3048 people pass filters and QC.

Should I keep files with the same individuals between all files ? or is it ok to keep some individuals for a chromosome, which may not be present in the other chromosome. Thanks !

plink gwas • 2.5k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by nlehmann90
1

I would merge all into one binary (bed) file then do the QC, etc.

ADD REPLYlink written 3.6 years ago by zx87549.3k

How do you merge all files into one bed file ? with cat ? and you do this with bed and bim and fam files ? That would be very helpful if you'd be a little more specific. Thanks !

ADD REPLYlink written 3.6 years ago by nlehmann90

Plink is very well documented, see Merge multiple filesets

ADD REPLYlink written 3.6 years ago by zx87549.3k

If you are performing a single SNP analysis, generally it is not necessary to have the same number of samples for each variant.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by christopher medway440
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