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Answer: Encountering Error while Running 'make vcf' in Biostar Handbook
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@ialbert ,I am deeply immersed in the fog and request the help ,please
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are you sure bedtools can handle the non-standard location of strand information?
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Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly.
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```bash
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Did it affect the bamtofastq output file? if so how did you solve the problem?
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You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
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Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
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