User: bruce.moran

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bruce.moran670
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Posts by bruce.moran

<prev • 120 results • page 1 of 12 • next >
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Comment: C: Recommendations for Whole Genome Sequencing Workflow
... Sarek includes GATK 'best practices' but is a lot more than just that. ...
written 7 days ago by bruce.moran670
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Answer: A: Recommendations for Whole Genome Sequencing Workflow
... Based on your affiliation (cancer center) you might want to look at [Sarek][1] which is a pipeline for WGS data offering both somatic and germline variant calling. [1]: https://github.com/nf-core/sarek ...
written 13 days ago by bruce.moran670
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Comment: C: Classifying normal vs cancer tissues from mutational data
... Yes, with some GI polyps for example this is the case too, but the point holds that it is not really appropriate to generate sequencing data from any kind of pre- or tumourous material without first having a pathologist review it. You waste time and resources trying to answer this kind of question. ...
written 19 days ago by bruce.moran670
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Comment: C: Classifying normal vs cancer tissues from mutational data
... This issue should be resolved before any sequencing data is generated, typically by pathologists. As you say 'this tissue should be cancerous', then you should have that checked by going back to where that tissue was processed, and asking those who did that. ...
written 20 days ago by bruce.moran670
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Comment: C: How to download BCL files from NextSeq run?
... Old thread, but can you specify how you got to BCL through basemount? ...
written 5 months ago by bruce.moran670
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Answer: A: How to find those files name which contains specific symbol i.e. underscore sign
... > so now i want to extract those files names (like abc00001.keg) which don’t contains underscore sign _ in 2nd column of each files. for x in *.keg; do TEST=$(cut -f 2 $x | grep _ | head -n1) if [[ $TEST == "" ]];then echo $x; fi done ...
written 5 months ago by bruce.moran670
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Comment: C: Need help understanding ARACNe-AP output
... You need to find 'master regulators' using for example [viper][1] [1]: https://www.bioconductor.org/packages/release/bioc/html/viper.html ...
written 6 months ago by bruce.moran670
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Comment: C: Ploidy for variant calling in tumor pooled samples for amplicon next-generation
... For both MuTect2, HaplotypeCaller (no experience with FreeBayes) > Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). So DNA was pooled, libraries made and sequenced? The four tumours are all from the same individual? Is the amplicon panel only on the ...
written 8 months ago by bruce.moran670
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Comment: C: GATK4 VariantRecalibrator resource error
... Don't do much germline mutation calling, but I think ExAC might have superseded HapMap? No idea WRT `-comp`. I highly recommend [the GATK website][1], it's a bit of a mess because of versioning but the users and mods are very active, and because it's GATK your error will have occurred for others and ...
written 9 months ago by bruce.moran670
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Comment: C: GATK4 VariantRecalibrator resource error
... Have a look at [this thread][1] Basically you need a `:` between resource parameters and the resource path: --resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0:/xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf Although this also depends on your version of GATK... [1]: ...
written 9 months ago by bruce.moran670

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