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Specific chromosome run

See original GitHub issue

Dear Kishwar,

I am wondering how to run PEPPER variant calling on a BAM file with only focusing for a specific chromosome like chr20? Thanks.

Issue Analytics

State:
Created 2 years ago
Comments:11 (4 by maintainers)

Top GitHub Comments

1reaction

tahashmicommented, Apr 19, 2022

@renzhiyang I didn’t resolve this issue yet. I think there is some TensorFlow version issue in DeepVariant-2.0.0 and above with TensorFlow installed on our HPC. PEPPER-r0.4 is working fine with DeepVariant-1.0.0.

0reactions

renzhiyangcommented, Apr 20, 2022

Hi @tahashmi, thank you so much for your reply. I will have a try on PEPPER-r0.4.

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