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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 5 months ago by Raony Guimarães • 1.1k
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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 5 months ago by Raony Guimarães • 1.1k
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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 6 months ago by Raony Guimarães • 1.1k
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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 9 months ago by Raony Guimarães • 1.1k • updated 9 months ago by ATpoint ♦ 29k
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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 11 months ago by Raony Guimarães • 1.1k
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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 11 months ago by Raony Guimarães • 1.1k
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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 13 months ago by Raony Guimarães • 1.1k
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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 13 months ago by Raony Guimarães • 1.1k
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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 13 months ago by Raony Guimarães • 1.1k • updated 13 months ago by zx8754 ♦ 9.0k
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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 14 months ago by Raony Guimarães • 1.1k

Latest awards to Raony Guimarães

Voter 11 months ago, voted more than 100 times.
Guru 13 months ago, received more than 100 upvotes.
Teacher 13 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 14 months ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 17 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 23 months ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 23 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
Popular Question 2.2 years ago, created a question with more than 1,000 views. For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
Teacher 2.4 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
Teacher 2.6 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
Great Question 2.7 years ago, created a question with more than 5,000 views. For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
Teacher 3.0 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 3.7 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 3.9 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 4.1 years ago, created a question with more than 1,000 views. For Exome 101
Popular Question 4.2 years ago, created a question with more than 1,000 views. For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
Scholar 4.6 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
Popular Question 5.6 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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