User: Nandini
Nandini • 720
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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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... 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 29 days ago by
Nandini • 720
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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 29 days ago by
Nandini • 720
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... Have you tried GEO or dbGAP ?
Also, why are you using a subset of IGAP only ? All of IGAP summary stats are here : [IGAP][1]
[1]: http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php ...
written 4 weeks ago by
Nandini • 720
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... thank you @lffu_0032 , the link provided is useful! ...
written 4 weeks ago by
Nandini • 720
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... Yes, done that [already][1]
[1]: https://gatkforums.broadinstitute.org/gatk/discussion/13553/difference-in-haplotype-caller-gatk4-vs-3-7#latest ...
written 5 weeks ago by
Nandini • 720
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... Hello
Does anyone know the difference/updates for Haplotypecaller in GATK v4 vs GATK 3.7 ?
I am not able to find anything specific in terms of its algorithm or major changes in the walker on the GATK website
Thanks, ...
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Comment:
C: CNV and pseudogenes
... well we are still doing MLPA. Cannot rely on an invalidated CNV pipeline ...
written 11 weeks ago by
Nandini • 720
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Comment:
C: CNV and pseudogenes
... of course, we MLPA everything before reporting but also trying to build a reliable bioinformatics pipeline ...
written 11 weeks ago by
Nandini • 720
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Comment:
C: CNV and pseudogenes
... True, I agree but we are more in a clinical setting than research so its generating data per panels.. i guess it's just finding an appropriate way of deal with this in a diagnostic environment ...
written 11 weeks ago by
Nandini • 720
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... Hello,
I'm using ExomeDepth to detect CNVs and I'm providing a bed file for all our targeted gene panels.
We know there is a processed pseudogene in a region, am just wondering if this would confound CNV calling in other genes? If it knocks off the ‘average’ coverage ?
Is it worth excluding su ...
written 11 weeks ago by
Nandini • 720
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