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I'm seeing an error that looks like it involves 'N' bases (see stack trace below). Not sure if the Ns are in the ref genome (we're using b37) or the BAM file, but either way this is a showstopper since we can't guarantee that either will never have a N.
Here's the stack trace:
Traceback (most recent call last):
File "/opt/clair/clair/../clair.py", line 93, in <module>
main()
File "/opt/clair/clair/../clair.py", line 87, in main
submodule.main()
File "/opt/clair/dataPrepScripts/ExtractVariantCandidates.py", line 450, in main
make_candidates(args)
File "/opt/clair/dataPrepScripts/ExtractVariantCandidates.py", line 290, in make_candidates
base = BASE2ACGT[SEQ[query_position]]
KeyError: 'N'
Really awesome work otherwise! I think your approach has a lot of advantages over the DeepVariant method (which seems a lot just like an improved VQSR), I'm pretty excited about Clair in general!
The text was updated successfully, but these errors were encountered:
I'm seeing an error that looks like it involves 'N' bases (see stack trace below). Not sure if the Ns are in the ref genome (we're using b37) or the BAM file, but either way this is a showstopper since we can't guarantee that either will never have a N.
Here's the stack trace:
Really awesome work otherwise! I think your approach has a lot of advantages over the DeepVariant method (which seems a lot just like an improved VQSR), I'm pretty excited about Clair in general!
The text was updated successfully, but these errors were encountered: