User: Raony Guimarães
Raony Guimarães • 1.1k
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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
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... Hi Kevin, thank you so much for this elaborate answer! I keep finding your posts whenever I look for a solution to my problems. :D ...
written 6 weeks ago by
Raony Guimarães • 1.1k
2
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1
answer
1.0k
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1
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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 16 months ago by
Raony Guimarães • 1.1k
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1.9k
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... 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 16 months ago by
Raony Guimarães • 1.1k
0
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13k
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... Hi Kevin, Just a small typo, it's actually:
`gunzip human_g1k_v37.fasta.gz ;` ...
written 17 months ago by
Raony Guimarães • 1.1k
1
vote
2
answers
928
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2
answers
... > 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 20 months ago by
Raony Guimarães • 1.1k
• updated
20 months ago by
ATpoint ♦ 44k
1
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0
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... 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 23 months ago by
Raony Guimarães • 1.1k
0
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2
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33k
views
2
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... 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 23 months ago by
Raony Guimarães • 1.1k
0
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2
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2.6k
views
2
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... You could merge the files with bcftools:
bcftools merge -O z -o merged.vcf.gz sample1.vcf.gz sample2.vcf.gz ...
written 2.0 years ago by
Raony Guimarães • 1.1k
4
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3
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1.0k
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3
answers
... A map of constrained coding regions in the human genome
https://www.nature.com/articles/s41588-018-0294-6 ...
written 2.0 years ago by
Raony Guimarães • 1.1k
12
votes
3
answers
1.0k
views
5 follow
3
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... 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 ...
written 2.0 years ago by
Raony Guimarães • 1.1k
• updated
2.0 years ago by
zx8754 ♦ 9.9k
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