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ukhsa-collaboration / snapperdb

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Can't populating database with VCF #25

Open phongphak opened 5 years ago

phongphak commented 5 years ago

Hi,

I've generated VCF files from single-end FASTQ using PHEnix pipeline. Then I tried to add them to database and I got this message:

Namespace(command='vcf_to_db', config_file='/home/user/software/snapperdb-1.0.6/user_configs/H99_config.txt', force='N', log_dir='/home/user/software/snapperdb-1.0.6/log/', vcf=['/home/user/cryptococus/vcf/ERR2624140.filtered.vcf'])
Calulated depth is not calculated - cuttoff is 30
Average depth below cutoff, not added to SNPdb
### Completed 2019-08-25 15:33:20.193076

So as you see depth wasn't calculated even though I lower the cutoff or using option -f FORCE

Do you have any idea on this issue?

timdallman commented 4 years ago

Hi, Can you confirm the version of PHEnix please? Can you attach the filtered VCF please? Thanks Tim