User: Raony Guimarães

gravatar for Raony Guimarães
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Dublin / Ireland
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raonyguimaraes
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PhD in Bioinformatics with experience in developing software and methods to the fields of Precision Medicine and Pharmacogenomics.

Currently working for a company called Genomics Medicine Ireland developing Bioinformatics software for doing NGS analysis.

Posts by Raony Guimarães

<prev • 81 results • page 1 of 9 • next >
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Answer: A: convert VCF to gVCF
... You cannot convert a VCF to gVCF. For generating a gVCF you need a BAM file. The difference between a VCF and a gVCF is that on the gVCF you have the counts for each base that are equal to the reference genome for all the sites where you don't have a variant. You cannot get that without having the ...
written 10 months ago by Raony Guimarães1.1k
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Answer: A: How to download dbSNP153 vcf files in hg19/GRCH37 version
... I don't think there is one available at the moment, but you can first get one for hg38: wget -4 -c https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz wget -4 -c https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz.tbi Then, liftover it ...
written 10 months ago by Raony Guimarães1.1k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hi Kevin, Just a small typo, it's actually: `gunzip human_g1k_v37.fasta.gz ;` ...
written 10 months ago by Raony Guimarães1.1k
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Answer: A: BCL files as deliverables from a sequencing center
... > Is this something sequencing providers or core facilities usually give > their customers? No, this is not very common but I can understand why someone would ask for that. (i.e. They prefer to do sample demultiplexing themselves adjusting the penalty parameters or use a different software ra ...
written 13 months ago by Raony Guimarães1.1k • updated 13 months ago by ATpoint36k
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Comment: C: How to create 1000G_phase1.snps.high_confidence.hg19.sites.vcf ?
... Here you find an explanation about what makes it having high confidence: https://media.nature.com/original/nature-assets/nature/journal/v491/n7422/extref/nature11632-s1.pdf It was a combination of multiple strategies. ...
written 16 months ago by Raony Guimarães1.1k
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Comment: C: Convert VCFf file to plink ped/map format while filtering the SNPs
... I think you need samples in your vcf to calculate the minor allele frequency. If you are using --allow-no-samples your vcf might have no samples to calculate it from. ...
written 16 months ago by Raony Guimarães1.1k
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Answer: A: How to combine a multi sample VCF from multiple sample VCF?
... You could merge the files with bcftools: bcftools merge -O z -o merged.vcf.gz sample1.vcf.gz sample2.vcf.gz ...
written 18 months ago by Raony Guimarães1.1k
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Answer: A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... A map of constrained coding regions in the human genome https://www.nature.com/articles/s41588-018-0294-6 ...
written 18 months ago by Raony Guimarães1.1k
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Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2018?
... What do you think were the most influential Bioinformatics/Computational Biology Papers/methods/discovery Of 2018? Previous Discussions [What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2017?][1] [What Are The Most Influential Bioinformatics/Computational Biology Paper ...
bioinformatics forum papers survey snp written 18 months ago by Raony Guimarães1.1k • updated 18 months ago by zx87549.4k
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Answer: A: Redundant Group Of Proteins.
... I would try to find the minimum amount of common proteins between the 24 organisms. ...
written 18 months ago by Raony Guimarães1.1k

Latest awards to Raony Guimarães

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Machine Learning Tutorials In Python
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Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Scholar 18 months ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Scholar 2.3 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Popular Question 2.6 years ago, created a question with more than 1,000 views. For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
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Great Question 3.1 years ago, created a question with more than 5,000 views. For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Scholar 4.1 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
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Popular Question 4.6 years ago, created a question with more than 1,000 views. For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
Scholar 5.0 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
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Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File

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