Hello hive mind,
I work with segmented virus and normally I uses freebayes to make the vcf file, bgzip and tabix to compress and index and then the
standard cat ref.fa | bcftools consensus vcf.file > cns.fa to make a consensus. This has worked for years, but now after upgrading to 1.7 from 1.3 this no longer seems to work.
My ref.fa file has 10 individual segments in it and the expected output would be a cns.fa file with 10 individual segments, with variant calls however I am only receiving the last segment now.
I have also tried using
bcftools consensus -f ref.fa -o cns.fa vcf and this gives the same answer as before, just one segment.
I can write a script to loop through all the regions if I need to, but I wanted to see if someone here had a solution that just uses the tools as is.