(--blocks no-pheno-req) command is not working in plink 1.07

[Rasha Saleh]

Hello everybody,

I am a new user to plink and the version I am using in my University cluster is plink 1.07. I am analysing data from  1K genome project, with missing phenotype data. I tried to do haplotype block estimation, but didn't work due to the missing phenotype data, so I tried adding this command (from plink 1.9 documentation);

plink --bfile myfile --blocks no-pheno-req

 

but the error i got is: ** Unused command line option: no-pheno-req

I am aware of the change in the functionality and command line usage between different plink versions, but downloading a new version will take a long time due to security policies in my university. Can anyone help with writing this command in a format that is acceptable to plink 1.07?

Thanks

[Christopher Chang]

plink 1.07 does not have this option.  Easiest workaround is to set all the phenotypes to e.g. '1'.

[miqui rumba]

Hello, I am trying to convert a plain text imputation to plink1.9 with --23file ( I have not map file). I need skip INDELs like these wich stop convertion, thanks

MERGED_DEL_2_2432 1 25591101 G

MERGED_DEL_2_2433 1 25591901 G

Missatge de Christopher Chang <chrch...@gmail.com> del dia dc., 28 de nov. 2018 a les 20:37:

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[Christopher Chang]

Add "--snps-only no-DI".

On Wednesday, November 28, 2018 at 12:50:10 PM UTC-8, miqui rumba wrote:

Hello, I am trying to convert a plain text imputation to plink1.9 with --23file ( I have not map file). I need skip INDELs like these wich stop convertion, thanks

MERGED_DEL_2_2432 1 25591101 G

MERGED_DEL_2_2433 1 25591901 G

Missatge de Christopher Chang del dia dc., 28 de nov. 2018 a les 20:37:

plink 1.07 does not have this option.  Easiest workaround is to set all the phenotypes to e.g. '1'.

On Wednesday, November 28, 2018 at 4:40:51 AM UTC-8, Rasha Saleh wrote:

Hello everybody,

I am a new user to plink and the version I am using in my University cluster is plink 1.07. I am analysing data from  1K genome project, with missing phenotype data. I tried to do haplotype block estimation, but didn't work due to the missing phenotype data, so I tried adding this command (from plink 1.9 documentation);

plink --bfile myfile --blocks no-pheno-req

 

but the error i got is: ** Unused command line option: no-pheno-req

I am aware of the change in the functionality and command line usage between different plink versions, but downloading a new version will take a long time due to security policies in my university. Can anyone help with writing this command in a format that is acceptable to plink 1.07?

Thanks

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