Question: Plink SNP association with Drug Sensitivity Resistance Testing values
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gravatar for kokyriakidis
27 days ago by
kokyriakidis0 wrote:

Hi everyone!

I have 170 samples. For each sample I have a vcf file with the SNPs and an other file with values corresponding to Drug sensitivity values for 500 drugs.

The final files are:

File2:

FID IID/Drug Drug1 Drug2 Drug3. ..... Drug500 0 Sample1 0.8 0.4 ........ ...... 0.9 0 Sample2 0.3 -9 ........... ........... 0.3 . . . 0 Sample170

and the merged vcf file for all samples

FIle1 (vcf):

Chr Pos ... Sample1 Sample2 ... Sample170 1 1 1 . . . . . Y

Can you help me on how to make association between specific SNPs and the abberations (changes) in drug sensitivity of a particular drug?

Do I have to use a command like this? Is this right? Have you other suggestions?

plink --vcf-half-call r --const-fid 0 --vcf MERGED.vcf.gz --pheno DrugSensitivityAnalysisFinal.tsv --allow-no-sex --all-pheno --linear --pfilter 5e-4 --ouT results

sequencing snp next-gen genome • 60 views
ADD COMMENTlink modified 27 days ago • written 27 days ago by kokyriakidis0
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