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I have dots instead of values in the quality field (QUAL) in my vcf

Hello guys, I'm new to bioinformatics. I don't know exactly how to deal with vcf files. In the context of a study I'm working on. I generated a vcf file, and when I looked at it I found out that I have dots instead of values in the quality field (QUAL). So For that, I'm stuck now.

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written by wirefox • wirefox

How did you generate the VCF? Please show all commands that were used, if possible.

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written by Kevin Blighe Kevin Blighe

Hello Kevin,

I generated my VCF with VCFHUNTER. I used the following commands:

qsub -pe parallel_smp 30 -q long.q -b yes -V -N file-vcf "python3 /directory/bin/process_reseq_1.0.py -c file-conf -p file-vcf -s f -t 30"

qsub -pe parallel_smp 30 -q long.q -b yes -V -N file-vcf "process_reseq_1.0.py -c file-conf-41an.tab -p file-vcf -s f -t 30"

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written by wirefox • wirefox

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