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Problem with ambiguity characters in v0.5

See original GitHub issue

Hi,

I am currently running PEPPER v0.4 for some Illumina-corrected ONT reads (Guppy 3.6) of HG002 and the results are very good. On chr1:0-5,000,000, F-measure is 98.78% with the CCS mode and 98.18% with the ONT mode.

I tried PEPPER v0.5 this morning on the same raw and corrected data, no change in parameters:

PEPPER v0.5 does not output any variants for the corrected data in ONT mode (while v0.4 did). It seems pepper_variant has some errors of the type ERROR IN THREAD: 'M'. My corrected ONT reads do indeed contain ambiguity characters in some reads as SNP candidates that couldn’t be corrected with enough accuracy. Is it a problem in this new version?
I ran PEPPER v0.4 and v0.5 on the raw ONT reads for the same region. v0.4 gives me 97.57% F1 while v0.5 gives me 96.63% F1, so a non-negligible decrease of performance with this new version.

Thank you for the help!

Guillaume

Issue Analytics

State:
Created 2 years ago
Comments:8 (4 by maintainers)

Top GitHub Comments

1reaction

kishwarshafincommented, Sep 2, 2021

@GuillaumeHolley , I have pushed the new docker.

Please run:

docker pull kishwars/pepper_deepvariant:r0.5

And then run:

time docker run -it -v /data:/data \
kishwars/pepper_deepvariant:r0.5 \
pepper_variant --version

This should give you PEPPER VERSION: 0.5.2 which should have your issue fixed. Please feel free to reopen if you face any other issues.

0reactions

GuillaumeHolleycommented, Oct 11, 2021

I can confirm here the new version works fine with ambiguity characters.

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