Melanie Lou

Hi Adam, For each call, coverage is reported. However I notice that there tend to be more reads shown in IGV than what is reported as coverage for a region in a VCF. How do you calculate coverage (or which reads do you not include and why)? Best, Melanie

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....

Let me reiterate what you're saying. As long as I have reference coordinate (i.e.,...

Hi Adam, I'm confused regarding the spots output with respect to insertions. In honeyExample,...

Hi Adam, Of the insertions called, here are two examples: 1 20096231 1:20096231_N/<INS>...

Solved: It turns out PyIntervalTree is needed even if I have intervaltree and intervaltree-bio...

Hi Adam, I have intervaltree (2.1.0) and intervaltree-bio (1.0.1) installed in my...