I downloaded a fasta file with a consensus sequence and a vcf file with the variant for certain individual (both files from 1000 genomes). I'm trying to get the sequence for that individual. To do that, i'm using vcf-consensus like this (let's say the consensus is master.fasta and the vcf is HG02291.vcf.gz):
tabix -p vcf HG02291.vcf.gz
cat master.fasta | vcf-consensus HG02291.vcf.gz > HG02291.fasta
After I do that, I compare HG02291.fasta with master.fasta and they are the exact same files (same headers and sequences), therefore vcf-consensus is not applying any changes to master.fasta. I've tried the same procedure with many other samples and it still does not work. What am I doing wrong?