Applying full support for the IUPAC nucleotide code standard for better robustness?

[Jia-Xing Yue]

Hello,

I am got the following error when testing clairvoyante on my data. By examining where the error occurs, I guess this error could be solved by applying full support to the IUPAC nucleotide code standard? Thanks in advance!

Loading model ...
Traceback (most recent call last):
File "/home/jxyue/Projects/Varathon/build/conda_clairvoyante_env/bin/dataPrepScripts/ExtractVariantCandidates.py", line 312, in
main()
File "/home/jxyue/Projects/Varathon/build/conda_clairvoyante_env/bin/dataPrepScripts/ExtractVariantCandidates.py", line 308, in main
MakeCandidates(args)
File "/home/jxyue/Projects/Varathon/build/conda_clairvoyante_env/bin/dataPrepScripts/ExtractVariantCandidates.py", line 169, in MakeCandidates
pileup[pos][base] += 1
KeyError: 'Y'

Best,
Jia-Xing

[Ruibang Luo]

@chaklim Fix to be included in Clairvoyante 2. The proposed solution is to convert any IUPAC code in the reference input to the first matching alphabetical base pair as recommended in the VCF 4.3 specification

[Jia-Xing Yue]

Hi @aquaskyline ,

Thanks for the instant reply and information! Is there an expected release schedule for Clairvoyante 2 ?

Best,
Jia-Xing

[Ruibang Luo]

At the bottom of Clairvoyante's readme, there is a link to a newer version.

…

On Thu, Oct 10, 2019 at 8:48 PM Jia-Xing Yue ***@***.***> wrote: Hi @aquaskyline <https://github.com/aquaskyline> , Thanks for the instant reply and information! Is there an expected release schedule for Clairvoyante 2 ? Best, Jia-Xing — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#41?email_source=notifications&email_token=AAG2SONWFHPE3EFFT4SJXZ3QN4QBPA5CNFSM4I7MHGP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEA4EKQY#issuecomment-540558659>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG2SOI2FX55U33DAPJ6R5LQN4QBPANCNFSM4I7MHGPQ> .

-- Laurent

[Ruibang Luo]

Resolved in Clair.