Comments (2)
Hi Erik,
the variant is killed due to very low base alignment quality (BAQ; see https://www.ncbi.nlm.nih.gov/pubmed/21320865), which is computed on the fly by LoFreq (using samtools routines). If you switch its use off (-B) you get the variant. This usually means there is a base alignment issue, e.g. ambiguity due to a nearby indel. Having said this, I can't see an indel or repetitive sequence in that region. This will require debugging in samtools will therefore take some time...
In the meantime: if you are confident enough about your mapping (and have for example realigned your BAM file with e.g. LoFreq viterbi) you can switch BAQ off with -B (just like in samtools)
Thanks for reporting
Andreas
from lofreq.
closing due to inactivity
from lofreq.
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