Hello,
I am using samtools/bcftools 1.2 and i would like to ask if there is a way
to call a "N" for a NOT COVERED site. At the moment 'bcftools consensus'
outputs REF whenever the site is not in vcf file as if there were a
consensus. I would also say it's a BUG since vcf2fq just actually uses an
"N" in this case.
Thanks in advance.
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