User: geocarvalho

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geocarvalho70
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Posts by geocarvalho

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Plotting common SNPs from four individual from a vcf file
... http://bioinformatics.psb.ugent.be/webtools/Venn/ I normally use it ...
written 4 days ago by geocarvalho70
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Answer: A: Packages/modules for CNV, Indels, SNPs analysis
... See this repository: # [ThousandVariantCallersRepo](https://github.com/deaconjs/ThousandVariantCallersRepo) ...
written 18 days ago by geocarvalho70
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Answer: A: R books with Quantitative Genetics examples?
... Books with bioinformatics content and R that I know: 1. [Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools](https://www.amazon.com.br/Bioinformatics-Data-Skills-Reproducible-Research/dp/1449367372) 2. [R Programming for Bioinformatics](https://www.crcpress.com/R-Pr ...
written 18 days ago by geocarvalho70
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Comment: C: vcfeval Error: No sample name provided but calls is a multi-sample VCF
... About your other comment. If you have a VCF with mulitple samples you must choose one at a time. For example: * For a header: `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_1 Sample_2 Sample_3` command: ``` ./rtg vcfeval --baseline=reference.vcf.gz --bed-regions=roi.bed -c merged_extra.vc ...
written 7 weeks ago by geocarvalho70
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Answer: A: vcfeval Error: No sample name provided but calls is a multi-sample VCF
... Your VCF header label has the same name of the file? For example: `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GIAB_MY_region` `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT merged_extra` or is another? Because the label expected for the `--sample` argument is the label present in the VCF header. ...
written 8 weeks ago by geocarvalho70
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Answer: A: List all available databases for ANNOVAR
... I had to use a directory to store the data ``` $ perl annotate_variation.pl -downdb -webfrom annovar avdblist humandb/ -buildver hg19 ``` So you can open this file ``` $ more humandb/hg19_avdblist.txt ``` ...
written 9 weeks ago by geocarvalho70
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Answer: A: How to start analyzing next-generation DNA and RNA sequencing data?
... As you are familiar with R, see [Harvardx](http://rafalab.github.io/pages/harvardx.html) classes. I also recommend starting reading [Biostar Handbook](https://www.biostarhandbook.com/). Nowadays, I'm migrating my shell/python pipelines to [pipeline frameworks](https://www.ncbi.nlm.nih.gov/pubmed/2 ...
written 4 months ago by geocarvalho70
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Answer: A: Extract Sub-Set Of Regions From Vcf File
... bedtools intersect worked better to me `intersectBed -a input.vcf -b /path/to/my.interval.bed -header > output.vcf` ...
written 4 months ago by geocarvalho70
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Comment: C: Bioinformatics Data Analyst, University of Pennsylvania, Philadelphia
... I would like to try, how can I do it? ...
written 10 months ago by geocarvalho70
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Answer: A: Where can I find a sample analysis pipeline for DNA?
... More examples of pipeline that you can extract some analysis are [SpeedSeq][1], [bcbio][2] and [IMPACT-pipeline][3]. [1]: https://github.com/hall-lab/speedseq [2]: https://github.com/chapmanb/bcbio-nextgen [3]: https://github.com/rhshah/Exome-Pipeline ...
written 10 months ago by geocarvalho70

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