Low coverage and confidence

[freconfarmer]

Amazing little program!

A few questions

1. The difference from raw to mapped was 81% from my Nebula results. There was a warning before finishing that stated low coverage, confidence low. Would you trust this result? Smn 1=1 Smn2 =1 Would it still be safe to say is a carrier with warning and low confidence?
2. The confidence was set at 1 for all. What is a perfect score?
3. I used a Bam file that was converted from the Cram using WGS Extract. Would the Cram file with reference produce a better result?

Thanks for your time!

Conrad

[xiao-chen-xc]

Hi Conrad,

Are you using a full WGS bam? What is your sequencing coverage? The warning may suggest something suspicious. If you like, you could send me your .json output file, either attaching it here or emailing me at chenxecho@gmail.com.

Thanks,
Xiao

[freconfarmer]

Hi Xiao,

I am using a 30X WGS bam from Nebula. It was a conversion from the cram by WGS Extract. I'm not sure of which reference genome it used, but it appears as "hs38(Chr), rCRS, 195 SNs" on the stats. Sequencing coverage was 81% with an average read of 29X. I will send you an email of the .json file. For some reason it isn't being recognized to copy.

Thanks

Conrad