User: donutbrew

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donutbrew10
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10
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New User
Location:
Atlanta, GA
Last seen:
4 days, 4 hours ago
Joined:
2 years, 3 months ago
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c*****@gmail.com

Posts by donutbrew

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Comment: C: Confused about how to generate a consensus sequence after bwa
... AFAIK, you can't use a modified reference genome with bcftools consensus. You'll get an error like "The fasta sequence does not match the REF allele at..." and the consensus output will die at that point (where the 'N' is in the reference). I You CAN, however, generate the pileup with the masked re ...
written 7 days ago by donutbrew10
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Comment: C: generating a reasonable consensus with bcftools + vcf-consensus
... I'm also having this issue. There doesn't seem to be any prebaked solution to converting an mpileup to a consensus sequence that will include both SNPs and INDELs. Even when I can see the deletion in the alignment in igv, and the pileup recognizes it, the resulting vcf going through bcftools gets ri ...
written 2.3 years ago by donutbrew10

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