User: keeley.brookes

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Posts by keeley.brookes

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Answer: A: Freebayes coverage enquiry
... Thanks Jen, Thats very helpful. Is there a glossary somewhere on galaxy for terms like this, as they don't always mean what you think they mean and it would be really helpful for a novice like me. ...
written 7 months ago by keeley.brookes0
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Freebayes coverage enquiry
... Silly question time: I have been using Freebayes to find variants in my data, using the simple setting with filtering. When setting the min coverage level i have been using 10. thinking this meant that it needed a minimum of 10 total reads to evaluate the site for a SNP. However some of the out ...
freebayes read coverage dp count written 7 months ago by keeley.brookes0
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How can I annotate a vcf file created with Freebayes with rs#
... Hi All, I have a vcf file created in freebayes (v.0.0.2), and I would like to annotate the file with rs# id so I can filter them out and obtain just a list of novel variants. I have tried to use VCF-VCF intersect but I don't think it has given me what I want. The final aim is to create a file wi ...
annotate vcf annovar dbsnp snpeff written 8 months ago by keeley.brookes0 • updated 8 months ago by Jennifer Hillman Jackson25k
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BAM file problems, sorting filtering and running naive variant called
... Hi All I have aligned by RNA-seq using BWA for Illumina - as I would like to use Naive Variant Caller downstream. I converted my BWA SAM files to BAM files, and merged the four technical replicates I had. I them sorted the file - using SAM tools and although green it had this error attached Ign ...
nvc hisat2 freebayes variant rna-seq written 8 months ago by keeley.brookes0 • updated 8 months ago by Jennifer Hillman Jackson25k

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