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Use bcftools isec to find denovo mutations

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?

mutations denovo
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updated by Ram 4.5K • | written by anasjamshed 14

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

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written by anasjamshed 14

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

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written by Pierre Lindenbaum 17K

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".
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written by anasjamshed 14

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

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written by anasjamshed 14

I am using ubuntu through windows sub sytem

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written by anasjamshed 14

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

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written by anasjamshed 14

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

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written by anasjamshed 14

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

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written by anasjamshed 14

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.

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written by Ram 4.5K

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