Andreas Wilm

Not calling insertions on NC_000912_Mpneumoniae

2

Deletions are working fine, e.g. NC_000912.1:782755 T>TAG See /data/out/NC_000912_Mpneumoniae Indel qual shows up as 0: `lofreq call -f $REFFA -b NC_000912_Mpneumoniae_comb.lf3.bam -r NC_000912.1:782754-782755 --loglevel 3 -p -P`

cd /data/out/NC_000912_Mpneumoniae REFFA=/data/lofreq3-testdata/NC_000912_Mpneumoniae/NC_000912_Mpneumoniae.fasta lofreq call -f $REFFA -b NC_000912_Mpneumoniae_comb.lf3.bam -r NC_000912.1:782755-782755 --loglevel 3 -p -P

Base qualities are always present as per SAM standard. For indels they might be missing. LoFreq currently happily calls indels with missing quals, which should probably only be possible when...

Previously part of #27

Extra: publish as notebook?

Currently the extra data is filtered in slidingDeque.nim():posWithinRegion. This will be especially inefficient for piling up long reads

`./lofreq call -f tests/denv2-simulation/denv2-refseq.fa -b tests/denv2-simulation/denv2-10haplo.bam -r "gi|158976983|ref|NC_001474.2|:52-52"` predicts var at 51