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cpwardell / FiNGS

Filters for Next Generation Sequencing
Apache License 2.0
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CRITICAL ERROR: unreadable VCF file: name 'vcfcount' is not defined #11

Open gudeqing opened 1 year ago

gudeqing commented 1 year ago

Hi, I am struggling with filtering large number of false positive variants from output of Vardict-Java, and find this very good tool may be helpful for me. Now, I am using the docker image cpwardell/fings:latest, but encountered the error as following at the very begining.

"CRITICAL ERROR: unreadable VCF file: name 'vcfcount' is not defined"

I think the problem is in line 41 of /opt/conda/lib/python3.8/site-packages/fings/FiNGS.py, there "vcfcount" will not be available directly.

Best regards!

ZeTTeRNooB commented 4 months ago

Sure, have a same problem. Please, can someone help? vcfcount also, isn't a standart command for python or pyvcf.