What Does The Plink Error: "Could Not Place Marker For Left Window Edge" Mean?

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9.8 years ago

roll ▴ 350

Hi,

I keep getting the following error message from plink:

ERROR: Could not place marker for left window edge

Does anyone know what does this error means?

Thanks in advance

plink • 2.3k views

ADD COMMENT • link updated 9.8 years ago by Istvan Albert 98k • written 9.8 years ago by roll ▴ 350

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Can you add the command you are trying to run?

ADD REPLY • link 9.8 years ago by zx8754 11k

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I am running the following command --file myFile plink --linear --pheno myPhwno --mpheno 3 --missing-phenotype -9 --missing-genotype N --chr 5 --from-bp 100 --to-bp 200 --out myplinkOUT --hide-covar --covar myCov

ADD REPLY • link 9.8 years ago by roll ▴ 350

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Maybe there are no SNPs in that region? There are also options for Mb, Kb --from-kb, --from-mb.

ADD REPLY • link 9.8 years ago by zx8754 11k

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Can i do something about this? tell plink to ignore this for example? As I would like to keep my window range small.

ADD REPLY • link 9.8 years ago by roll ▴ 350

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How do you mean "ignore"? Maybe --silent

ADD REPLY • link 9.8 years ago by zx8754 11k

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As far as i know, plink not always report results from snps. How can i make it to report association results even if there is no snp?

ADD REPLY • link 9.8 years ago by roll ▴ 350

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If there are no SNPs in that region, you still want association results based only on covariates? I don't think this can be done in plink.

ADD REPLY • link 9.8 years ago by zx8754 11k

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