User: Raony Guimaraes
Raony Guimaraes • 100
- Reputation:
- 100
- Status:
- New User
- Location:
- Website:
- http://www.torchmed.com
- Last seen:
- 8 years, 5 months ago
- Joined:
- 8 years, 9 months ago
- Email:
- r************@gmail.com
Posts by Raony Guimaraes
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... Hello, I end up using a lot more VariantAnnotator from GATK to treat my VCF files against anything I really want. I gave up using vcf-annotate, it's not very functional...
Right now I'm annotating using 1000genomes(nov2011), dbsnp135, Exome Variation Server, snpeff. And after this I also created a ...
written 8.4 years ago by
Raony Guimaraes • 100
• updated
11 months ago by
RamRS ♦ 28k
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... Sooner than later U$1000 genomes has arrived to our lifes! What is going to be the impact of this to the field of Bioinformatics ? I just would like to hear some comments about this news from people in here. Does anyone know more about the technology ?
Source:
http://news.jornal.us/article-6108.Ion ...
written 8.6 years ago by
Raony Guimaraes • 100
• updated
4.7 years ago by
Biostar ♦♦ 20
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... May be you could do something like this:
grep "^#' yourFile.vcf > newvcffile.vcf
grep -v "^#" yourFile.vcf | awk '{printf $1, $3, $2, $4... }' >> newvcffile.vcf ...
written 8.6 years ago by
Raony Guimaraes • 100
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... Hello I'm trying to convert my vcf file from 1000 genomes pilot study 2 (trios) that I believe was annotated with hg18 to hg19 using this Broad Tool:
http://www.broadinstitute.org/gsa/wiki/index.php/LiftOverVCF.pl
At this directory I found:
ftp://ftp.broadinstitute.org/Liftover_Chain_Files/
Inde ...
written 8.7 years ago by
Raony Guimaraes • 100
• updated
5.8 years ago by
Biostar ♦♦ 20
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... Where I can find dbsnp135 ?
This address still not updated:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz
...
written 8.7 years ago by
Raony Guimaraes • 100
• updated
2.4 years ago by
Biostar ♦♦ 20
3
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... Hello I'm looking for a dataset of snps from patients with breast cancer to compare with snps from normal patients. I only could find affymetrix data and it's about 7GB per patient on GWAS Studies. I would like to compare using only about 500 snps not 500k from > 100 patients.
Is there a way to ...
written 8.7 years ago by
Raony Guimaraes • 100
• updated
8.4 years ago by
Chris Miller ♦ 21k
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