How to intersect data from four different annotated files using ubuntu commands?

Question

[otokha]

I have three affected and one unaffected VCF and annotated files from exome analysis. I want to compare the variants present in the affecteds and absent in unaffected data.

How can I pull out the variants unique to affected individuals from all the four files?

Kindly help.

Answer 1

[Pierre Lindenbaum]

merge the vcf files with bcftools and the use an expression to test the 3 affected genotypes and the non-affected genotype:

bcftools merge src/test/resources/S[1-4].vcf.gz | \
bcftools  view -i '(GT[0]=="AA" || GT[0]=="RA")  && (GT[1]=="AA" || GT[1]=="RA") && (GT[2]=="AA" || GT[2]=="RA") &&  (GT[3]=="RR" )'

[otokha]

Thanks for the help. GT[1] == "AA" represents the missing variants among the affecteds data, is it?

[Pierre Lindenbaum]

AA = "alt+alt" homozygous for the alternative allele(s)

[otokha]

Thanks for timely help.

[WouterDeCoster]

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