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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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nanopolish variants vs freebayes #1135

Closed emilydolivo97 closed 2 months ago

emilydolivo97 commented 3 months ago

Hello ,

I have 11 FASTQ files. I have already used FreeBayes to detect variants. For this purpose, I utilized the following command for each FASTQ.gz file:

freebayes -f user/ref_genome/reference_sequence.fa -L SRAXXXX87.fastq.gz --vcf SRAXXX87.vcf --ploidy 2 --min-alternate-fraction 0.05

Now, I want to know what s the equivalent of this command using Nanopolish. Is it nanopolish variants --consensus or nanopolish variants without consensus? If it is, how do I use it please?

I hope that you could help me !!**

jts commented 3 months ago

Nanopolish requires the raw signal data in fast5 format. If you only have fastq you can't use nanopolish.