Entering edit mode
10.9 years ago
Sheila
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420
I have a number of VCF files, each that have two columns of sample data. I'd only like to take ONE of those two columns and load into a project. Is it possible to do this in plink seq? If so, how? I haven't been able to find any documentation on this.
Dear Sheila, this question has been asked multiple times here before. I would like to ask you to use the site search. To avoid further redundancy, I have closed the question. You will possibly find an answer in Extracting columns from VCF file using vcftools/perl, Extracting info from a column of vcf file?, or Select certain column from vcf file
This question specifically addresses how to subset VCF data with PLINK/SEQ. Plink/SEQ allows you to import a whole VCF file into a "project". From here, users can do a number of data manipulation methods etc, however I want to just import 1 column of genotypic sample data into the project itself. I haven't seen any information of how to do this with the specific tool. I ask that this question be re-opened.
I do not have an answer to your question, but your question made me learn about plink/seq. It seems a nice tool, thank you for making me discover it :-)
Sorry, missed that.
No problem! Thanks!
Just in case you do not find the solution, using one of the other options to prepare a filtered VCF might be an option.