Bcftools allele frequency

Question

[switch.reem]

Dear all

Can you please help me analysing a VCF file. I want to use bcftools isec option to check the difference in values in allele frequency for two VCF files at common locations. So can you please help me with the parameters?

Answer 1

[Pierre Lindenbaum]

 join -t, -1 1 -2 1  \
           <(bcftools query -f '%CHROM-%POS-%REF-%ALT,%INFO/AF\n' input1.vcf | sort -t, -k1,1)  \
           <(bcftools query -f '%CHROM-%POS-%REF-%ALT,%INFO/AF\n' input2.vcf | sort -t, -k1,1)

[switch.reem]

Thank you so much. So this will extract the allele frequency in the two vcf files based on matching positions? But how do I find if their values are different?

[Pierre Lindenbaum]

awk -F, '($2!=$3)'

[switch.reem]

Thank you so much. This is very useful

[Pierre Lindenbaum]

It it answered your question , please validate (green mark on the left) to close the question.