User: Nandini
Nandini • 760
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Bioinformatician
Develop and maintain pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis
Posts by Nandini
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... Have you tried [UCSC table browser][1] ?
[1]: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=711027113_pLhHGH6YmOysUzCgwrfAnskhsBBg ...
written 7 days ago by
Nandini • 760
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... It should work for all chromosomes. Does your vcf input file have all chromosomes ? ...
written 9 days ago by
Nandini • 760
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... tried that - there is no download option for files there ...
written 27 days ago by
Nandini • 760
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... I thought so... Okay, I'll try getting in touch with HGMD. ...
written 27 days ago by
Nandini • 760
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... @finswimmer, I do not know how the file looks like - hence the question.
I would like to know the file format and if its compatible to use in such annotation tools.
I have been asked to incorporate this into our variant annotation pipeline and HGMD pro licence is not free, so before we apply, I wa ...
written 27 days ago by
Nandini • 760
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... Hello,
does anyone here use the HGMD pro flat file? Can I know the format of the flat file and if I can incorporate it within annovar for variant annotation ?
Many thanks ...
written 27 days ago by
Nandini • 760
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Comment:
C: Extract info on OMIM Phenotype
... thank you so much! This works perfect! ...
written 4 weeks ago by
Nandini • 760
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... Hello,
I have around 900 gene symbols and its Gene ID (HGNC) for which I need to extract all its corresponding OMIM phenotype. Is there a way to do it or a tool that does this ?
For example, *ABCA1* with HGNC ID 13666, the info to extract is listed here in column "[Phenotype][1]"
Thank you,
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... Most of it depends on the aim of your project. What are you trying to achieve from your GWAS study ? Is there an aim to this project ? ...
written 3 months ago by
Nandini • 760
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... all SNPs in IGAP identified to date are "susceptible loci" -> meaning there are mostly likely to be associated with a RISK of developing late onset Alzheimer's . The link in my comment above gives you the data or the summary statistics for IGAP.
IGAP was a big study that constituted of many many ...
written 3 months ago by
Nandini • 760
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