Concordance Using Plink

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12.5 years ago

P.NJ ▴ 50

I am trying to find the concordance for a sample (SOLiD data for a whole genome) against its Array data generated from Illumina 2.5M. To do this, I am using plink, but when I used this command

plink --bfile file1 --bmerge file2.bed file2.bim file3.fam --merge-mode 7 --out myfile1vs2

I get

Concordance rate is nan

Is my data wrong or my command ?

plink solid array • 6.3k views

ADD COMMENT • link 12.5 years ago by P.NJ ▴ 50

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hard to tell with this information. how did you created the file1 files? Plink will match by SNP id so if you didn't label your SOLiD SNPs with the rs ids on the array data then there is nothing to compare. your command is correct so there must be something wrong with the data.

ADD REPLY • link 12.5 years ago by Adrian Cortes ▴ 550

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well there is an in house tool which can convert SNPs into PLINK format. For the array data I used the lgen format. The SOLiD SNPs are names with the rs ids. i checked the bim files as well, the snps are in the form of rs ids and some of them are in this format : snp1_554484

ADD REPLY • link 12.5 years ago by P.NJ ▴ 50

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