The only code that appears to work for me when I want to generate consensus sequences have been:
samtools mpileup -Q 20 -q 20 -d 5000 -uf ref.fa sorted.bam | bcftools call -c | vcfutils.pl vcf2fq -d 10 -Q 20 -l 1 > consensus_output.fq
However, I don't need ambiguity and almost every spot in the alignment across my samples have ambuiguous data but I want it to just give me the top called base. Even if it was 50/50 between two bases I need it to just give me one or the other. Anyway to insert this into the line of code above?
Literally has been the only code that worked on my data using samtools and bcftools v 1.8. I'm not even using the -i option which says to use IUPAC so why am I getting it???