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Question: removing duplicate SNPs (same position) with lowest call rate
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gravatar for jani.p.heikkinen
5.0 years ago by
jani.p.heikkinen • 0
jani.p.heikkinen • 0 wrote:

I am trying to solve a problem with my genotyped array data set. For reason or another, the data set has duplicate or with three different names pointing to the same position. For example:

index SNP pos A1 A2 F_MISS
2046 snp_1 113890304 C T 0
2047 snp_2 113890304 C T 0.000422
2048 snp_3 113890304 C T 0

I want to build a list for SNP names to be removed (so I can exclude them in PLINK).

So from the SNPs above, snp_1 or snp_3 and snp_2 should be in removal list.

How would I achieve this?

 
snp genome • 1.9k views
ADD COMMENT • link •
modified 4.2 years ago by Biostar ♦♦ 20 • written 5.0 years ago by jani.p.heikkinen • 0
0
gravatar for TriS
5.0 years ago by
TriS • 4.3k
United States, Buffalo
TriS • 4.3k wrote:

if you just want to remove duplicates in R (not tested):

name_position <- apply(mySNPmatrix,1,function(x) paste(x[2],x[3],sep="_"))
mySNPmatrix <- mySNPmatrix[-which(duplicated(name_position)),]

however, it seems that the F_MISS col is not duplicated, so pay attention to that when removing rows
ADD COMMENT • link written 5.0 years ago by TriS • 4.3k
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gravatar for christopher medway
5.0 years ago by
christopher medway • 450
Cardiff, UK
christopher medway • 450 wrote:

Try this bash one-liner (not tested). You may need to loose the header line though.

sort -k 3 -k 6 input.txt | awk '!seen[$3]++' | awk '{print $2}' > output.txt
ADD COMMENT • link written 5.0 years ago by christopher medway • 450
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