bcftools isec output for multiple vcf files interpretations

bcftools isec output for multiple vcf files interpretations

0

I have four vcf files resulting from mutect2 function. There is one treatment and three control samples. I need to get variants that are unique to the treatment plus variants that are common in all four vcf files files(treatment and control samples). To do so, I first the following command:

bcftools isec -n~1000 -c both treatment.vcf.gz control1.vcf.gz control2.gz control3.vcf.gz -p result

The output contaigns four files from 0000 to 0003.
And then

bcftools isec -n~1111 -c both treatment.vcf.gz control1.vcf.gz control2.gz control3.vcf.gz -p result2

And then merge the results of these commands to single vcf file. But as there are four vcf files from each commadn I dont know which one shpould I choose. Any idea


gatk


mutect2


calling


bcftools


variant

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