Moderator: Dan Gaston

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Dan Gaston6.8k
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Canada
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Last seen:
23 hours ago
Joined:
6 years, 2 months ago
Email:
d************@deaddriftbio.com

Clinical Laboratory Bioinformatician and Assistant Professor. Department of Pathology, Nova Scotia Health Authority and Dalhousie University. Next-generation sequencing-based molecular diagnostics with a focus on cancer genomics and transcriptomics. Genomic analysis of rare Mendelian diseases. Some analysis and work with bacterial and viral genomics. A passion for software development. Particularly web-services, visualization, project-management, and analysis pipelines.

PhD background in phylogenetics and molecular evolution. Focused on functional divergence and subcellular localization, analysis of next-generation sequencing data.

Posts by Dan Gaston

<prev • 840 results • page 1 of 84 • next >
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Answer: A: Meaning of 'tag' in the context of variants
... It is explained right in the text and answered by Jean-Karim above. The SNP that is being picked up as being associated with the phenotype is not causal but is in Linkage Disequilibrium with the true causal SNP. This is a pretty routine thing for GWAS analyses. ...
written 23 hours ago by Dan Gaston6.8k
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Answer: A: calculate average target coverage from bam file
... While there are other tools to do the job, the issue is you appear to have 1) a mismatch between the installed version of samtools and where you are taking your appropriate command from and 2) your command line for specifying the input files is incorrect. The -a option is only found in the newer ver ...
written 9 days ago by Dan Gaston6.8k
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Comment: C: VCF merge containing CNV
... Structural variants, including CNVs, have been allowed in VCFs according to the specification for quite some time. You can get into adding custom tags for ease of use (like SVEND is often used to give easy reference to stop coordinates). While it may well be that a caller may be adding custom fields ...
written 16 days ago by Dan Gaston6.8k
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Answer: A: VCF merge containing CNV
... Whether vcf-merge works for what you are doing or not I'm not actually sure off hand. However, since you have a solution you have tried the answer is to test that solution. Take some sample VCFs with the type of variants you want to merge, run vcf-merge, and look at the results. Do you get what you ...
written 16 days ago by Dan Gaston6.8k
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Comment: C: HaplotypeCaller filter out variants covered only in one direction
... I think you misinterpreted my meaning. In all cases the OP wants to use StrandBias as a filter. However, if you are working with any form of hybridization data you absolutely should be doing duplicate removal. If you are working with amplicon data you should skip doing duplicate removal because you ...
written 4 weeks ago by Dan Gaston6.8k
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Comment: C: HaplotypeCaller filter out variants covered only in one direction
... You do want to calculate StrandBias, unless you are doing amplicon sequencing though you absolutely do not want to remove duplicate filtering. That is just adding noise and bias into your data. ...
written 4 weeks ago by Dan Gaston6.8k
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Comment: C: Programming Language In Bioinformatics
... PyCharm is a great development environment, but yes it won't teach you Python. There are probably dozens, if not hundreds, of online courses you can do for free to learn Python. Depending on what you want to do you'll even find some geared towards Data Science type analyses versus standard things. C ...
written 5 weeks ago by Dan Gaston6.8k
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Answer: A: Script to run on linux for assembly on clusters
... Well, it partially depends on your cluster. Since you have DIDA installed, the abyss command itself has a dida subcommand you can use as per the manual and documentation. There does appear to be an abyss-dida wrapper script ([abyss-dida on github][1]) but I'm not sure exactly how it is used as I hav ...
written 12 weeks ago by Dan Gaston6.8k
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Comment: C: Which source of annotation files to use, Ensembl or UCSC?
... It does (and I preferentially use Ensembl as well) but it should be pointed out that many of the transcripts in particular have very weak evidence, and can interfere in some cases with proper assignment of specific base pairs to the canonical gene. That said I still prefer it, because it is more com ...
written 3 months ago by Dan Gaston6.8k
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Answer: A: Pindel and GATK AD Concordance
... I have a somatic variant caller that merges variant calling from six different variant callers, and having them calculate different VAFs is pretty normal. Each caller has its own (sometimes tunable) criteria for inclusion/exclusion of reads or bases for instance, and in somatic variant calling this ...
written 3 months ago by Dan Gaston6.8k

Latest awards to Dan Gaston

Scholar 5 weeks ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 3 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 4 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 6 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Popular Question 10 months ago, created a question with more than 1,000 views. For Gatk'S Unifiedgenotyper And Genotype Determination
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Use Conservation Or Evolutionary Rate To Infer Functional Relevance Of Aminoacid
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Popular Question 11 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Scholar 13 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Scholar 13 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Popular Question 13 months ago, created a question with more than 1,000 views. For Gatk'S Unifiedgenotyper And Genotype Determination
Scholar 13 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Use Conservation Or Evolutionary Rate To Infer Functional Relevance Of Aminoacid
Popular Question 14 months ago, created a question with more than 1,000 views. For Gatk'S Unifiedgenotyper And Genotype Determination

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