User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver3.5k
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1 month, 3 weeks ago
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5 years, 9 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 • 388 results • page 2 of 39 • next >
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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 4 months 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 4 months 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 4 months ago by Brice Sarver3.5k
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Answer: A: GFF file for soybean RNAseq analysis
... [The Ensembl page for Glycine max][1]. You can find GFF3s under 'Gene annotation.' [1]: http://plants.ensembl.org/Glycine_max/Info/Index ...
written 4 months ago by Brice Sarver3.5k
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Answer: A: Remote blast of SRA database
... The SRA-searching blastn is part of sra-tools. Check out the [blastn README on sra-tools' Github][1]. Note that the SRA objects are prefetched. [1]: https://github.com/ncbi/sra-tools/blob/master/README-blastn ...
written 4 months ago by Brice Sarver3.5k
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Comment: C: /bin/bash/ command not found
... Okay. I assumed the /bin/bash/ extra '/' was a typo, but check out RamRS' suggestion below. ...
written 5 months ago by Brice Sarver3.5k
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Answer: A: Is there any tool available to generate ultrametric tree from a rooted phylogene
... If you're unwilling to or can't calibrate your phylogeny by placing prior distributions on node ages in [BEAST][1] (for example), you can try using a few other approaches. Nonparametric rate smoothing is implemented in the R package [ape][2]. This is also implemented in [r8s][3], along with PL and M ...
written 5 months ago by Brice Sarver3.5k
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Comment: C: /bin/bash/ command not found
... If you type `which bash`, what do you get? Perhaps your system has bash installed outside of /bin/. ...
written 5 months ago by Brice Sarver3.5k
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Answer: A: How to Read Alleles in Samtools
... Check out the manual page of [samtools mpileup][1]. It may be easier to use [samtools view][2] to subset on positions of interest and explore those to see what's going on to convince yourself that you're looking at the right things. Also, check out [IGV][3] for a nice way to visualize BAMs. [1] ...
written 5 months ago by Brice Sarver3.5k
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Comment: C: PhD Bioinformatics on GWAS
... Not sure what you mean. Are you considering developing new methods/applications/statistical approaches? There's definitely work to be done to move things forward. [Check out the Future Perspectives section in this paper][1]. [1]: https://www.frontiersin.org/articles/10.3389/fpls.2019.00100/full ...
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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