can i merge many vcfs or I should do in realignment?
Hi I have 50 whole genome sequence data for SNP discovery. somebody say to me you should use all samples together for realignment and if I do realignment Separately for each sample then my results of SNP discovery will be wrong. I want to know is it true?
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Siavash Salek Ardestani •
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Siavash Salek Ardestani •
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Do you have each sample in a separate VCF file? I ask because your post title mentions merging VCF files and your actual post has nothing on that.
yes. I would appreciate you guide me.
in realignment step I could realignment all samples together, then I had one bam file for SNP discovery .on the other hand I could realignment each sample separately. I want to know the result of these methods for SNP discovery is different?
I don't really know what that means, but AFAIK samples get realigned independently, giving you one BAM per sample. I am not sure if this information helps you.