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Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
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Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
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Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
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I supect your reads are hard clipped. Show us the first lines of
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Here you go.
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Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant.
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That turns it into a mess of paragraphs, but if it truly is more productive thanks for the tip!
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Please show us your full annovar command line.
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Did you get this figured out? I am having the same error in R.
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Try this:
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