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As a follow-up, is it possible to get a variant call if rather than N, I have one of the ambiguity codes (e.g. R, Y, B etc) in the referenc…
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The GATK (and afaik every caller that I know) treats every contig of the reference as having the same ploidy (so all haploid, all diploid, …
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Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
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Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are pai…
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Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
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Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
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Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
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Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
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Thank you Ram for the comments! Noted for future posts.
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