Question: Count SNPs using bcftools
0
gravatar for usukjung
19 days ago by
usukjung0
usukjung0 wrote:

I have 3 bam files (5kgeneration, 15kgeneration, and 50kgeneration) and merged them into a VCF file with a reference genome. I would like to count SNPs between the 3 samples in a VCF file using bcftools. For example, Between 5k and reference, how many SNPs? Between 5k and 15k, how many SNPs?

snp • 125 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 20 • written 19 days ago by usukjung0

See this topic

ADD REPLYlink written 18 days ago by brunobsouzaa350

Thank you for sharing the link. If possible, could explain it more? I am a beginner so I cannot get a picture...

ADD REPLYlink written 18 days ago by usukjung0

Basically, you can use the tool to split your file into subjects that you want to analyse and perform comparison into those files. Check bcftools and/or vcftools manuals to see how to use them.

ADD REPLYlink written 18 days ago by brunobsouzaa350

Okay. So Is there any way to compare them without splitting file?

ADD REPLYlink written 18 days ago by usukjung0

There is... Take a look into bcftools or vcftools manual.

ADD REPLYlink written 15 days ago by brunobsouzaa350

I know but I am just a beginner who wants to learn the code. I have never handled it until now so I asked questions... If you don't want to help me out, hm... thank you

ADD REPLYlink modified 12 days ago • written 12 days ago by usukjung0

Learning the code doesn't mean that we need to give you all codes that you need... If you really want to learn, read the manuals, understand how the software work, and how it fits to your purposes. I can give you a code that doesn't fit your purposes and you would need to debug it! So, again, read the manuals and learn how softwares work. You won't find on the internet codes that do exactly your job!!! That's all help I can give you! Good luck!

ADD REPLYlink written 12 days ago by brunobsouzaa350

Also, I gave you the exact solution, all you have to do is read the manual... Codes are in there, all you have to do is type it into your terminal with appropriate changes. Show some effort, don't expect someone to just give you all solutions!

ADD REPLYlink written 12 days ago by brunobsouzaa350
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