User: Brice Sarver

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Brice Sarver3.5k
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3,450
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Last seen:
15 hours ago
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5 years, 5 months ago
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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 • 385 results • page 1 of 39 • next >
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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 1 day 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 1 day 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 4 days 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 days 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 days 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 8 days 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 9 days ago by Brice Sarver3.5k
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Comment: C: Merge VCF INFO tags
... My recommendation would be to do this in R or Python. VCFs are tabular, so you can easily manipulate the INFO field with `strsplit(..., split = "|")` or `.split('|')`, then apply whatever logic you want for the gnomAD annotation. ...
written 9 days ago by Brice Sarver3.5k
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Comment: C: merging vcf files with sample information
... The missing info means that a given variant was not in that particular VCF. In your example, 4/7 of your VCFs do not have variants called at that position, hence the missing genotype data. If you are expecting to have reference calls included as well, which aren't in VCFs by default, look into call ...
written 9 days ago by Brice Sarver3.5k
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Answer: A: merging vcf files
... From the [Picard documentation][1] for MergeVcfs: > Merges multiple VCF or BCF files into one VCF file. Input files must be sorted by their contigs and, within contigs, by start position. The input files must have the same sample and contig lists. An index file is created and a sequence dictiona ...
written 9 days ago by Brice Sarver3.5k

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Scholar 10 days ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: trimming fastq files with Trimmomatic
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