User: jsneaththompson

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Posts by jsneaththompson

<prev • 27 results • page 1 of 3 • next >
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Keep Format and Individual fields when annotating VCF with VEP
... I'm currently updating my Variant Calling Pipeline by switching the VCF annotating software from Annovar to VEP for a variety of regions, not least how easy it is to annotate with HGVS notation and keep datasets up to date in VEP. For the most part everything is running smoothly, with the exception ...
vcf annotation vep variant-calling written 11 weeks ago by jsneaththompson50 • updated 11 weeks ago by Emily_Ensembl15k
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Comment: C: hg19 or hg38 for variant calling
... The tool is LocatIt, which is used for deduplication of reads by the molecular barcodes used in the HaloPlex HS Target Enrichment System. https://www.agilent.com/cs/library/software/Public/AGeNT%20ReadMe.pdf ...
written 5 months ago by jsneaththompson50
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Comment: C: hg19 or hg38 for variant calling
... The tool is LocatIt, which is used for deduplication of reads by the molecular barcodes used in the HaloPlex HS Target Enrichment System. https://www.agilent.com/cs/library/software/Public/AGeNT%20ReadMe.pdf ...
written 5 months ago by jsneaththompson50
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hg19 or hg38 for variant calling
... I've recently been troubleshooting an error in part of my variant calling pipeline, which has been traced back to me using bam files aligned to hg38 as input for an Agilent deduplication tool which has yet to migrate from hg19 to hg38. Currently my workaround is to align to hg19, deduplicate, then s ...
genome variant calling assembly written 5 months ago by jsneaththompson50 • updated 5 months ago by h.mon16k
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Comment: C: VarDict Amplicon-Aware Calling with barcoded seq data
... There's no output when running that command ...
written 7 months ago by jsneaththompson50
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VarDict Amplicon-Aware Calling with barcoded seq data
... I'm trying out different variant calling software on non-matched somatic samples, where the pcr has been performed using an Agilent kit called Haloplex HS. At the moment I'm trying VarDict, and I want to try to run VarDict in amplicon-aware mode. The problem is, amplicon-aware mode requires a bed f ...
variant calling next-gen molecular barcode written 7 months ago by jsneaththompson50 • updated 7 months ago by Pierre Lindenbaum110k
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Comment: C: Making UpSetR plot with title
... I ended up going with a half-baked solution, although I used GIMP so I could match the font in the UpSetR plot to the title. ...
written 8 months ago by jsneaththompson50
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Comment: C: Making UpSetR plot with title
... It looks like you're right, I'll have to add the title after with some other method ...
written 8 months ago by jsneaththompson50
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Comment: C: Making UpSetR plot with title
... Unfortunately that doesn't work. UpSetR has options for main.bar.color, mainbar.y.label, and mainbar.y.max, so calling main results in `Error in upset(...) argument 7 matches multiple formal arguments` ...
written 8 months ago by jsneaththompson50
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Making UpSetR plot with title
... I'm using UpSetR to create UpSet diagrams [like this][1], but I can't find a way to add a main title to the plot. Does anyone know if this functionality is possible in the UpSetR package at the moment? [1]: http://caleydo.org/assets/images/projects/upset//upsetr-banana.png ...
R upsetr plot written 8 months ago by jsneaththompson50 • updated 8 weeks ago by scott.lohr0

Latest awards to jsneaththompson

Scholar 8 months ago, created an answer that has been accepted. For A: Issues installing Pindel from git

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