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It is possible to make "known indels" and "dbsnp" databases optional in this pipeline as was done in Sarek? #118

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Jokendo-collab opened this issue Jan 26, 2024 · 3 comments
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enhancement Improvement for existing functionality

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@Jokendo-collab
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Description of feature

I am working with zebrafish genome and it lacks "known indels" and "dbsnp" databases and I see it is a mandatory requirement in this pipeline. How can one call variants from an organism lacking the above mentioned files?

@Jokendo-collab Jokendo-collab added the enhancement Improvement for existing functionality label Jan 26, 2024
@bounlu
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bounlu commented Jan 26, 2024

Maybe you can provide a dummy empty VCF file for now to trick the pipeline?

@Jokendo-collab
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Not sure if that can work but I will give it a try

@bounlu
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bounlu commented Jan 26, 2024

It should work since that VCF will be used to substract the SNPs/indels only. So x - 0 = x meaning that you will get out back what goes in. Need to test to see how that will work though.

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