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?
•
written
by
switch.reem •
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)
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?
awk -F, '($2!=$3)'
Thank you so much. This is very useful
It it answered your question , please validate (green mark on the left) to close the question.
Log in to answer this question.
