Fluviewer currently groups ambiguous bases with low quality bases and masks them all with Ns. We are therefore losing this partial base call information.
Here, I add in logic to the analysis.py script that:
- changes
bcftools consensus command to incorporate ambiguous bases (-I flag)
- remove ambiguous base positions from the masked BED file
- change the VCF genotype field (GT) for ambiguous bases from
1 to 0/1 so that bcftools recognizes and incorporates them properly (necessary for ambiguity calling)
Fluviewer currently groups ambiguous bases with low quality bases and masks them all with Ns. We are therefore losing this partial base call information.
Here, I add in logic to the
analysis.pyscript that:bcftools consensuscommand to incorporate ambiguous bases (-Iflag)1to0/1so thatbcftoolsrecognizes and incorporates them properly (necessary for ambiguity calling)