Assigning separate samples to groups in a vcf file
I have some VCF files from several experiments, each containing multiple samples. I want to assign them into groups, according to the experimental setup.
How can I assign each sample to a group in VCF file, or should I do it during post-processing?
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How do you envisage this working, practically? Is it about re-ordering the samples in the VCF file? Is it about conducting statistical tests on the sample groups? please elaborate on what you are thinking.
It is about conducting statistical tests on the sample groups. I have poolseq data from 3 different groups that I want to compare, and 5-6 samples in each group. I have the VCF file that contains all of my samples.
You may consider SnpSift CaseControl, or converting your dataset to PLINK format and performing the statistical comparisons there.
I converted to PLINK format, it helped, thanks!