User: Peter vH

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Peter vH100
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http://www..sanbi.ac.za
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5 years, 5 months ago
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Posts by Peter vH

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Exclusive parameters in a workflow
... I implemented a solution based on my reading of what you have done: First, the tool: cwlVersion: v1.0 class: CommandLineTool inputs: touchparam: type: - type: record name: touchcode fields: touchcode: ...
written 4 months ago by Peter vH100
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Comment: C: BWA MEM vs BOWTIE2 , which is best?
... If you want to compare variant calling workflows, Brad Chapman's work with bcbio and comparing options might be useful to you. See: https://github.com/bcbio/bcbio_validation_workflows In essence what he did was to use the Genome in a Bottle NA12878 sample (http://jimb.stanford.edu/giab) and compare ...
written 6 months ago by Peter vH100
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Comment: C: intersect VCF files
... I installed `rtg-tools` 3.8.4 using bioconda. When I run `vcfeval` the output contains 4 VCFs: fn.vcf.gz fp.vcf.gz tp.vcf.gz tp-baseline.gz Judging from the slides and the preprint, the fn (false negative) file contains calls that are in the baseline but not in the calls file, the ...
written 10 months ago by Peter vH100 • updated 5 days ago by RamRS17k
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Where to find Drosophila melanogaster de novo transcript assembly data?
... I am studying de novo (non-model) genome annotation and would like to use a well characterised organism to test some of my methods. To this end I am looking for an assembled *de novo transcriptome* dataset for *Drosophila melanogaster*, preferably assembled from short read data. Does anyone know whe ...
drosophila assembly de novo transcriptome written 10 months ago by Peter vH100 • updated 3 months ago by jaudall0
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Comment: C: From multiple VCF files to multiple sequence alignment?
... So you'd do iterative vcf-consensus followed by MUSCLE? SNPhylo seems to do something like that. I'll experiment and compare it with the script I've written. ...
written 24 months ago by Peter vH100
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Comment: C: From multiple VCF files to multiple sequence alignment?
... I'm not quite sure how? The tools suggested in those threads, `vcf-consensus` and `FastaAlternateReferenceMaker` in the other, produce a single FASTA output from a single VCF input and don't deal with gaps created when considering the alignment between sequences having insertions and deletions. ...
written 24 months ago by Peter vH100
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From multiple VCF files to multiple sequence alignment?
... Hi there I have multiple VCF files generated from variant calling on sequenced bacteria (*M. tuberculosis*). I would like to create a multiple sequence alignment file (as a step towards computing a phylogeny of the samples) by combining the reference genome with the VCFs. Before I put time and effo ...
vcf alignment bacterial written 24 months ago by Peter vH100 • updated 22 months ago by Biostar ♦♦ 20
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Comment: C: Using the Directory type in Common Workflow Language
... Some of the CWL folks have directed "support" questions to Biostars recently on the understanding that when they get answered here the answers are easy for people to find in the future. I'll alert the community to this question though. ...
written 2.1 years ago by Peter vH100
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Comment: C: Using the Directory type in Common Workflow Language
... By the way I used this input to the above CWL: testdir: class: Directory location: file:///home/pvh/Documents/code/cwltool/foo ...
written 2.1 years ago by Peter vH100
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Using the Directory type in Common Workflow Language
... In trying to solve a problem posed by Stuti Agrawal, I've been trying to make a working example using the Directory type of CWL v1.0 as an input and not getting very far. I tried writing a tool that pics up the files from a Directory and adds them to a zip file. Note, this doesn't add the directory, ...
cwl written 2.1 years ago by Peter vH100 • updated 2.1 years ago by Michael R. Crusoe1.0k

Latest awards to Peter vH

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: BWA MEM vs BOWTIE2 , which is best?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: BWA MEM vs BOWTIE2 , which is best?
Scholar 4 months ago, created an answer that has been accepted. For A: Exclusive parameters in a workflow
Popular Question 5 months ago, created a question with more than 1,000 views. For Using the Directory type in Common Workflow Language
Popular Question 9 months ago, created a question with more than 1,000 views. For Using the Directory type in Common Workflow Language
Popular Question 9 months ago, created a question with more than 1,000 views. For Example cwl workflow (for v1.0)?

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