How to intersect data from four different annotated files using ubuntu commands?
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.
1 answer
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" )'
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Pierre Lindenbaum
AA = "alt+alt" homozygous for the alternative allele(s)
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Pierre Lindenbaum
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WouterDeCoster
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