Entering edit mode
3.6 years ago
usukjung
•
0
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?
See this topic
Thank you for sharing the link. If possible, could explain it more? I am a beginner so I cannot get a picture...
Basically, you can use the tool to split your file into subjects that you want to analyse and perform comparison into those files. Check
bcftoolsand/orvcftoolsmanuals to see how to use them.Okay. So Is there any way to compare them without splitting file?
There is... Take a look into
bcftoolsorvcftoolsmanual.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
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!
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!