Disabling dawnsampling in pepper_margin_deepvariant ?

[kiflu-23]

I need help!!
I am using pepper_margin_deepvariant variant calling for my target gene but PEPPER is not recognizing my region of interest where I did targeted sequencing using Nanopore. I think this is because of the dawnsampling. Is there anyway I can disable the dawnsampling? I tried to address it by changing --pepper_downsample_rate=0.02, but I am not sure if this is the right way or I am introducing bias?
Thank you in advance for your help.

[inari-ldavey]

I would like to know this as well, as the reported depth in my output vcf file does not correspond with the number of reads provided to PEPPER.

[kishwarshafin]

Oh, sorry, I misread the message. Is there a way you can see the depth of your sequencing in the region of interest on IGV or by running samtools depth? Also, downsampling happens at multiple places, in PEPPER and also in DeepVariant. It's to make sure we have a balanced runtime.

[kiflu-23]

Thank you for reply. Yes, I can see it, all my samples have more than 40k coverage. I downsampled the bam file to 100X. But I wanted to run the variant calling using the all the available reads. Is there a way to disable the dawnsampling?

Thank you

[kishwarshafin]

@kiflu-23 , in that case you'll have to run each step independently. First, collect all the commands that are run by running the run_pepper_magin_deepvariant with --dry-run command. Then for each pepper run, use --pepper_downsample_rate 0.0.

Also, we didn't see a big gain in accuracy after 60x-70x, so I am unsure if you'll get a big boost in accuracy after going through so many steps.