PBHoney spots parameters

Hi Adam,

I checked the documentation (HoneyReadme.txt and the url https://hgsc-vmweb-08.hgsc.bcm.edu/software/honey is down); please let me know if I should have looked elsewhere.

What do the following parameters mean?

-m MININDELERR, --minIndelErr MININDELERR
Minimum size of an indel error to be counted (5)
-e THRESHOLD, --threshold THRESHOLD
Minimum Spot Threshold (3)
--spanMax SPANMAX Maximum Size of spot to be called (3000)

For the following parameters, I believe -q uses MAPQ and -i uses szMean. Can you please confirm?

-q MINMAPQ, --minMapQ MINMAPQ
Minimum map quality of reads considered (1)
-i MININDELSIZE, --minIndelSize MININDELSIZE
Minimum indel SV size (50)

Self-explanatory:
-E MINERRREADS, --minErrReads MINERRREADS
Minimum number of reads with indel (3)
--consensus {pbdagcon,pbbanana,None}
Method for polishing consensus. (pbdagcon)

Much thanks,
Melanie

--minIndelErr, and insertion/deletion in the alignment needs to be over -m basepairs before we consider it for potential SV evaluation. This helps get rid of most of the sequencing errors since pacbio reads' main mistakes are single base pair insertions or deletions.

--threshold, is the minimum number of reads needed to support a varaint before it's considered for SV evaluation

--spanMax, if there's a region longer than this threshold where we have a signal of an SV, we ignore it.
This helps filter out extra-noisy alignment regions

--minIndelSize is the minimum size an evaluated SV needs to be before it's reported.

--minMapQ, correct. I put this at 1 by default because - generally - blasr reports a binary 0/256 MAPQ, so 1 helps filter out the handful of unconfident alignments.