User: Nandini

gravatar for Nandini
Nandini430
Reputation:
430
Status:
Trusted
Location:
UCL, London
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
5 years, 8 months ago
Email:
n********************@gmail.com

Bioinformatician

Develop pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis

Posts by Nandini

<prev • 108 results • page 1 of 11 • next >
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Answer: A: visualize CNV data based on WGS
... You can try [Alamut][1] We use it and it works quite well for large BAM files. [1]: http://www.interactive-biosoftware.com/alamut-visual/ ...
written 3 hours ago by Nandini430
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Answer: A: Association with snptest
... Yes, there are ways to do it. You can impute your data using the [Michigan server][1] [1]: https://imputationserver.sph.umich.edu/index.html ...
written 22 hours ago by Nandini430
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Comment: C: Mutect2 Usage, how can I make it work?
... Have you tried the [GATK forum][1] ? [1]: https://gatkforums.broadinstitute.org/gatk/discussion/8633/mutect2-sample-names ...
written 2 days ago by Nandini430
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Comment: C: Mapping from Human Exon 1.0 ST probeset IDs to Ensembl exon IDs
... Have you tried downloading a probeset annotation file from Affymetrix ? ...
written 5 days ago by Nandini430
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Comment: C: How can I generate a .vcf faster with GATK - HaplotypleCaller?
... GATK 4 has been officially released last evening already! :-) ...
written 6 days ago by Nandini430
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Comment: C: How to find (count) location/type of variant from a VCF file ?
... Try SNPEff if you need the count for the different types of variants. It also generates a html page for easy view of your results. Regarding FP and FN variants, look [here][1] [1]: https://www.biostars.org/p/187628/ ...
written 6 days ago by Nandini430
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Comment: C: How to find (count) location/type of variant from a VCF file ?
... If you have annotated the VCF file with annovar, your result/output file should already give you the different type/location of variants - that's generally what annotation tools do. If you want a detailed output, you can use VEP or SNPEff to annotate your file. ...
written 7 days ago by Nandini430
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Answer: A: How to extract SNPs from vcf file based on Population
... You can do this easily using vcftools, GATK tools, plinkseq etc. you first have to generate a text file with the list of samples that form the population of your choice, let's say "population_of_interest.txt" Then, vcf-subset -e -c population_of_interest.txt input.vcf > output.vcf or ...
written 7 days ago by Nandini430
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Comment: C: Computer specs for Bioinformatics
... Thank you everyone for your feedback! ...
written 5 weeks ago by Nandini430
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Comment: C: Computer specs for Bioinformatics
... Thanks genomax. We are not going to be analyzing or running NGS data on the computer. We have a huge cluster for that. This is just a desktop for minimum bioinformatics work/writing scripts/using IGV viewer and running small applications. As you can see, we are on a very tight budge of £1000 so not ...
written 5 weeks ago by Nandini430

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