I am generating consensus sequences using mpileup as per the web
samtools mpileup -uf test.fasta hits.bam | bcftools view -cg - |
This is working fine, but I am wondering of there is a way to force it to
call a regular base (ATCG) rather than what it currently does, an ambiguous
base, R,M,Y, etc, when the genotype is 50/50..
University of California- Berkeley
Museum of Vertebrate Zoology
Lab Website: http://ib.berkeley.edu/labs/lacey
Personal Website: http://macmanes.com/
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