User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver2.6k
Reputation:
2,620
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Trusted
Location:
United States
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Google Scholar Page
Last seen:
an hour ago
Joined:
4 years, 10 months ago
Email:
b***********@gmail.com

I'm a computational geneticist and bioinformatician working in industry. My background is in genomics, bioinformatics, and phylogenetics. AWS, R, Python, bash, relational databases, and Linux HPC environments.

Posts by Brice Sarver

<prev • 276 results • page 1 of 28 • next >
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Comment: C: PAML codeML 4.8 wont give maximum likelihood nor omega estimates
... 1) Do you have enough variability in your sequences? 2) Are you providing enough sequences at an appropriate tree height to expect to recover anything? 3) You're allowing more than one ratio among branches (model = 2) yet assuming a single rate among sites (NSsites = 0). Is this what you're trying t ...
written 4 hours ago by Brice Sarver2.6k
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Comment: C: BWA mapping parameters for DNA capture sequencing protocol
... Hopping in to provide support for ATpoint's comments - they're right. Map to the whole genome, then subset or restrict variant calling to regions of interest. You want your mapping qualities to reflect any uncertainty in genomic placement to produce the most accurate variant calls for your regions o ...
written 4 hours ago by Brice Sarver2.6k
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Comment: C: Nucleotide to amino acid conversion of multiple sequences
... So, you have multiple sequences with different start points relative to one another? Do you need to perform a multiple sequence alignment before translation, or has this already been done? ...
written 1 day ago by Brice Sarver2.6k
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Comment: C: vcflib-popstats to calculate FIS of a subpopulation
... Paging [Zev.Kronenberg][1]. [1]: https://www.biostars.org/u/3153/ ...
written 5 days ago by Brice Sarver2.6k
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Comment: C: FORMAT 'PL' is not defined in the header, assuming Type=String (bcftools)
... Have you tried defining PL in the header with your favorite plain text editor or using [bcftools reheader][1]? [1]: http://www.htslib.org/doc/bcftools.html#reheader ...
written 29 days ago by Brice Sarver2.6k
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Answer: A: how do you download a single SNP in vcf format?
... [bcftools view][1] will do this quickly and easily. [1]: http://www.htslib.org/doc/bcftools.html#view ...
written 29 days ago by Brice Sarver2.6k
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Answer: A: How to extract from a large text file in R
... Not enough information is given, but it sounds like they either want to subset or merge. Jean-Karim is right in this should likely be closed as off-topic. On the off chance that this is simply subsetting a large results file (say, ignoring headers), see below. Using data tables below, though data f ...
written 29 days ago by Brice Sarver2.6k
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Comment: C: Using samtools to view an indexed file in a private S3 bucket
... You're getting a permission denied error - have you confirmed that your ID and key have the appropriate privileges for the bucket and/or whether there are any other restrictions placed on the object? Can you see it if you use the AWS CLI (e.g., `aws s3 ls ...`? Do you need to change the [region for ...
written 4 weeks ago by Brice Sarver2.6k
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Comment: C: Multiple Sequence Alignment for >20 Sequences
... Are you aligning alignments or constructing MSAs from batches of genes/genomes? What's your input size? ...
written 4 weeks ago by Brice Sarver2.6k
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Comment: C: paired reads have different names
... Agreed. mm, please provide the BWA call. One input FASTQ or two? ...
written 4 months ago by Brice Sarver2.6k

Latest awards to Brice Sarver

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 4 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 8 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to construct a tree with MEGA when some of the sequences are very short
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Software for evaluating multiple sequence alignments before phylogenetic analysi
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to construct a tree with MEGA when some of the sequences are very short
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Identifying degenerate positions in Mus
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Quickly subsetting VCF while being memory efficient
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: split supermatrix by gene
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: The nucleotides on ENST00000347310 and ENST00000425614 do not agree on the same
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: trimming fastq files with Trimmomatic
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: trimming fastq files with Trimmomatic
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 2.7 years ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How to construct a tree with MEGA when some of the sequences are very short
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 2.8 years ago, created an answer that has been accepted. For A: Is there any way to quantify differences between neighbour-joining phylogenetic
Scholar 2.8 years ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree

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