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IUC (I talked to @bgruening) wants to adopt important tools from devteam repo in order to give them better treatment and maintenance. The MTS namespace is not a problem since we can upload/operate und…
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I have been using bamaddrg to assign tags to my four samples of sequence data, and then saved the output as a new .bam file rather than feeding it straight into freebayes.
The files parsed through …
EAC92 updated
4 years ago
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I installed snippy v 4.6.0 and snpEff version SnpEff 5.1d (build 2022-04-19 15:49). When the reference file is a .gb file, I encounter the following error
[19:30:07] This is snippy 4.6.0
[19:30:07] …
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hi, I'm using SeqLib via freebayes. I just unmounted the file system holding the bams that freebayes was accessing. but the program still had a 0 exit status.
I see this message:
`[E::bgzf_read] b…
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When trying to run snippy with calls to target sites of interest (in the form of a bed file), the freebayes-parallel part of the pipeline only works if the absolute path to the bed file is provide as …
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Freebayes outputs VCFs with genotype likelihoods of format GL (which are not phred scaled) instead of PL, but I found that demuxlet failed to produce reasonable results using those as the field input.…
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Freebayes comes up with "./." as a genotype. It probably means it can't score it(?). Bio-vcf needs to treat it as non-empty. Currently it sets everything to nil.
"./.:145.222:44:27:885:13:378:-10,0,-…
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Review existing tools in the pipeline if they can take in Nanopore data. If not, find a suitable alternative for long reads.
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Hey, I have 2 inquiries. I am running snippy to detect variance between multiple copies of the same part of a bacterial genome.
1. I saw the log (attached) of snippy and noticed the following command…
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I set the -t parameter to limit the variant calls to bed file containing the regions of interest. However, freebayes still calls variants outside the regions. The bed file is fine and it seems like th…