Use bcftools isec to find denovo mutations

Question

[anasjamshed]

I have 3 samples(N1,N2 and N3) in the trio_vcf file and to apply tools isec to find denovo mutations from these files Which command of isec tool should I use?

[Pierre Lindenbaum]

why isec when you can use dnm2 ? https://samtools.github.io/bcftools/howtos/plugin.trio-dnm2.html

[anasjamshed]

how can use it for 3 samples and find the common mutations?

[Pierre Lindenbaum]

"the common mutations" for a "denovo" ? whhaaat ?

[anasjamshed]

I got this error when I tried to run it: No functional bcftools plugins were found in

      BCFTOOLS_PLUGINS="path/to/plugin_dir".

- Is the plugin path correct?

- Run "bcftools plugin -lv" for more detailed error output.

Could not load "trio-dnm2".

[Pierre Lindenbaum]

https://www.google.com/search?q=+No+functional+bcftools+plugins+were+found+in

[anasjamshed]

How can I set up export BCFTOOLS_PLUGINS='path/to/plugin_dir'

[Pierre Lindenbaum]

https://www.google.com/search?q=+No+functional+bcftools+plugins+were+found+in

[anasjamshed]

I am using ubuntu through windows sub sytem

[anasjamshed]

I dont have PED file to run dnm2 . How can i make?

[barslmn]

You can find how in the documentation. Just find PED file in the page. https://samtools.github.io/bcftools/bcftools.html

[anasjamshed]

How? Please explain? Can i apply dnM2 directly on vcf file?

[anasjamshed]

I only have vcf file so can I apply trio-dmn2 on it

[Ram]

This is the result of very low effort from you - people are not motivated to help you out. Read as much documentation as you can and try solving your problem yourself. If you don't, that shows and we can only help you so far.