Torsten Seemann

@jackkamm are all the reads you are examining, do they have mapping quality >= 60 ? also, i realise freebayes uses orphan reads (no proper pair) which can cause problems....

Freebayes is run to use only MAPQ=60 and BASEQ=13 data to infer SNPs from. However it is using orphan reads from split pairs, which could be the problem,. I would...

Just found this too: "samtools 1.8 discards overlaps by default. Meaning that from two paired reads that cover a position, it will select only one, by increasing the base quality...

Chao No i have not! Thanks for the link! Torsten

homebrew-science is now defunct instead please use ``` brew untap homebrew/science brew tap brewsci/bio brew tap brewsci/science ``` and ``` brew install vt # or brew install brewsci/bio/vt ```

@pydupont thanks for the report - i think you've found a bug. i don't delete mlst.tab. I will fix. ``` again : (rm -fr roary/ roary_*/ report/ core.* *.gff {denovo,resistome,virulome}.tab...

What is nullarbor_translate doing?

@andersgs WARNING: i am now removing the final `quality` column from all tables. (It's a hack...) ``` my $nuke_last_col = $matrix->[0][-1] eq 'Quality'; # remove the Quality column from CSV...

WHoops, this removes it from the tables as well. Reverting for now. It needs to be put as a parameter to `$self->matrix_to_csv($matrix)`

Wrap in ` ` tags? `` but datatables controls it. ``