Query

[Cricetinae-hamster]

Hello,
I was wondering if would it be possible to skip a step, or a part of codoncounter algorithm if there are already generated vcf files, instead of starting from aligned bam files?

[codemeleon]

@Cricetinae-hamster. Currently, the option to bypass the Variant Calling step is unavailable. I can incorporate a feature to skip this step. However, BAM files will still be necessary along with user provided vcf files to generate statistics.

[jsan4christ]

Hi @ <https://github.com/Cricetinae-hamster>, can you also perhaps shed some more light on what you are trying to achieve? Are you looking at VCF files because of the difference in references used? or just prefer to start from VCF? We would like to better assist you. Please advise.

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