A bioinformatics tutorial on how to merge multiple vcfs using bcftools
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- เผยแพร่เมื่อ 30 ก.ย. 2024
- Where to download the vcf: evs.gs.washing...
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How to address the issue about "duplicated names" ? Is there a better way to solve that other than using --force-samples?
Thank you so much for the nice tutorial may you please explain what this ::: stands for and also -p?
may you please copy the link of the other video which you mentioned at the end of this session to compare the number of variants in the original vcf file and then merge ...? I could not find that video
Thank you so much for your effort, unfortunately the very last step didn't work but because of my files having duplicate samples
Hi how did you solve this issue?
Thank you so much 😀😀
Hi coach, can we unmerge the combined vcf file?
Yes. It can be done. You can split by chromosome or by sample ID or by variation type (snp, indels). I am currently working on videos for that
Hello! That's a wonderful tutorial. I just had one question though. Should the vcf files being merged have same header lines?
I have only experimented with chromosome and samples. So those are the headers I can only talk about. The headers (chromosome and samples) can be different With bcftools there are two types of merge commands. concat and merge. If the files have the same set of samples we use concat. If different samples or non-overlapping we use merge. I am currently working on a detailed video for the merging and will start posting soon.
@@bioinformaticscoach Ah that's still helpful! Thank you so much :D
@@bioinformaticscoach Hi, what is the name of this video (explaining the merge command). I can't seem to find it