Livius Penter

I just sent you an email with the reference I use as dropbox link to download. @AustinHartman

I have exactly the same problem when trying to deconvolute 2 donors based on their known genotypes. Interestingly, in one instance this has worked, but in other cases it didn't...

I am sorry for the confusion. I meant I am getting the same errors by souporcell as described by @Thapeachydude - I used cellsnp-lite to generate the vcf of the...

I just double checked - in the donor genotype vcf all fields have GT; I am able to run souporcell on the samples without the --known_genotypes option just fine

This is the command line error output: ```sh Traceback (most recent call last): File "/opt/souporcell/souporcell_pipeline.py", line 593, in souporcell(args, ref_mtx, alt_mtx, final_vcf) File "/opt/souporcell/souporcell_pipeline.py", line 531, in souporcell subprocess.check_call(cmd, stdout...

This is the first 50 lines of the donor genotype vcf - sample names I used should be correct (in fact I tried this also without supplying the sample names...

Ok, I'll put the relevant files into a dropbox and share it with you in a bit; I appreciate if you could take a look - I think your tool...

I don't know if you saw my email - I shared some data with you.

no worries - just wanted to make sure you got it; looking forward to any insights! :) get better soon

Interesting. It'd be great to keep those variants as simply removing seems like an expensive fix :). Thanks for looking into this!