User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver3.5k
Reputation:
3,510
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United States
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Google Scholar Page
Last seen:
2 months ago
Joined:
5 years, 10 months ago
Email:
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I'm a computational geneticist and bioinformatician working in industry. My background is in genomics, bioinformatics, and phylogenetics. Regularly use AWS, R, Python, bash, relational databases, and Linux HPC environments.

Posts by Brice Sarver

<prev • 388 results • page 1 of 39 • next >
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Answer: A: How can I make a BED file from a VCF file?
... Check out vcf2bed in [BEDOPS][1]. You can also try searching this site for more advice. [1]: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html ...
written 12 weeks ago by Brice Sarver3.5k
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Answer: A: How to detect different chromosomes from whole genome NGS reads of a fungi?
... 1. Use an assembler suitable for your data. Saying that it is paired-end isn't enough to evaluate how the libraries were prepared or what to expect. You mentioned SOAPdenovo2, so you've presumably started to explore this. 2. You can get a sense of the number of chromosomes by looking at related sp ...
written 4 months ago by Brice Sarver3.5k
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Answer: A: Cannot run HaplotypeCaller in GATK
... [AddOrReplaceReadGroups in the Picard manual][1] should tell you everything that you need to know. There's also a link to the GATK's definition list for more detailed explanations. You should also consider searching on Biostars - this has come up many times before. [1]: http://broadinstitute.gith ...
written 4 months ago by Brice Sarver3.5k
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Comment: C: How to Detect Frameshifts in a Protein Alignment
... What you tend to see if something is out of frame is an overrepresentation of stop codons in the downstream sequences - not always, but it acts as a good flag (especially if you're only expecting one and it's at the end of the string). You can explore this by looking at the first, second, and third ...
written 4 months ago by Brice Sarver3.5k
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Answer: A: How to Detect Frameshifts in a Protein Alignment
... What you're looking for is generally called a translation alignment. You'll start with a set of nucleotide sequences. These are converted to amino acids based on a translation table, aligned, and back-translated to their original nucleotides. This will make sure that the protein-coding genes are kep ...
written 4 months ago by Brice Sarver3.5k
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Comment: C: Good quality control metrics to look out for when someone gives you BAMs
... What quality metrics to look for, besides general run-specific metrics from the reads (e.g., the distribution of base qualities), will depend strongly on what's actually in the BAMs - WGS, WES, capture, amplicons, etc. For example, a high duplication rate may suggest libraries were overamplified for ...
written 5 months ago by Brice Sarver3.5k
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Answer: A: Bioinformatics Server on AWS
... I'm not a web app developer, but I'll list a few things off the top of my head re: compute and storage. You'll also need to set up a Virtual Private Cloud (VPC) and harden it using standard networking approaches. Instances are spawned into the default VPC unless another one is specified. Users and ...
written 5 months ago by Brice Sarver3.5k
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Comment: C: How can you update position field in a VCF?
... I'm not aware of an application that directly modifies the positions of the variants (alignment of indels excluded), but I'd be interested in hearing if anyone else has. If it were me, I'd simply process the VCFs as text (it's delimited after the header), looking for a chromosome/pos/ref/alt combin ...
written 5 months ago by Brice Sarver3.5k
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Comment: C: De novo assembly of paired end reads for small separate genes
... Ah, misread what you had. Thanks for clarifying! ...
written 5 months ago by Brice Sarver3.5k
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Answer: A: De novo assembly of paired end reads for small separate genes
... Check out the approach implemented in [ARC: Assembly by Reduced Complexity][1]. [1]: http://ibest.github.io/ARC/ ...
written 5 months ago by Brice Sarver3.5k

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Scholar 3 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
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