Problem with genome assembly de novo on STACKS
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3.6 years ago

Hi! I realized my genome assembly de novo in STACKS and I used this command to called the SNPs in VCF format.

populations -P ../stacks -M ../stacks/popmap.lst --fstats --vcf --genepop --threads 80

I have a problem with the VCF, I don´t have any value of quality (column "QUAL"), I don´t know what´s wrong.

Thank you so much! and please feel free to ask me any additional info.

assembly snp • 675 views
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Please provide more information. From the description it sounds like you are doing de novo genome assembly, but I can only assume you mean you are de novo assembling your RAD-Seq type reads with the de novo pipeline in STACKS (also not sure of the version of STACKS you are using or what commands you used to get to the populations step - those need to be provided too if you want any additional help). It is also very possible that there is no QUAL value for STACKS's VCF output. You could filter on other values such as DP, etc.

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