Looking-up SNPs within 16SrRNA from BED/bim/fam files

Question

[zizigolu]

Hi,

I have SNP genotypes for 50 individuals of 16SrRNA in BED/bim/fam and phenotype files.How I can extract SNPs from these files? Most of time log file says that

    Web-based version check ( --noweb to skip )
Connecting to web... Problem reading from SNPServer
    Recent cached web-check found...Problem connecting to web


Writing this text to log file [ F.log ]
Analysis started: Sat Nov 18 20:06:08 2017

Options in effect:
    --out F

PLINK-SNP (WGAS SNP annotation courtesy of Patrick Sullivan)
Connecting to web...

https://www.imageupload.co.uk/image/EDLP

Please somebody help me who knows why it sticks at Connecting to web...

Thank you

[WouterDeCoster]

It's checking its version online. Adding --noweb will disable that.

[zizigolu]

I added but sticks on Connecting to web...

Thank you

[WouterDeCoster]

Which version are you using? If not a recent one, you may want to upgrade.

[zizigolu]

Thank you, plink-1.07-dos, when I downloaded plink 2.00, plink.exe does not work

[WouterDeCoster]

plink.exe so you are on a windows machine then? ¯\_(ツ)_/¯

[zizigolu]

Yes, windows

says that Problem reading from SNPServer

[zizigolu]

I should write this command

--bfile C:\Users\Lenovo\Desktop\Microbiome_data\Microbiome_data\IPSEQ_Batch12_SNPQC_IPSeqID_IndQC
    --out C:\Users\Lenovo\Desktop\Microbiome_data\Microbiome_data\valid4
    --gplink

but this just worked for summary statistics