User: Garan

gravatar for Garan
Garan580
Reputation:
580
Status:
Trusted
Location:
United Kingdom
Website:
https://github.com/pasted
Last seen:
2 hours ago
Joined:
5 years, 5 months ago
Email:
g*********@gmail.com

Posts by Garan

<prev • 45 results • page 1 of 5 • next >
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Comment: C: Associate SNPs with Clinical Data
... Couldn't you use a large population study such as UK Biobank as your controls? There is some WES data (50K or so participants at this time, although all 500K should be done eventually), although you could just convert the variant calls from from the WES data to the SNP alleles that match the UK Biob ...
written 6 weeks ago by Garan580
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Comment: C: how to perform GWAS on UKBiobank data?
... You might want to try BOLT-LMM [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309610/][1], it's what we currently use for our analysis of UK Biobank data. We're also looking at using SAIGE but don't have the run times for UK Biobank yet. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309610/ ...
written 4 months ago by Garan580
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Comment: C: structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
... Isn't SVTYPE=CTX a hold-over from TIGRA-SV? Maybe it's due to support in GRanges readVCF for non-compliant VCF SV types? Not that this would help with BCFTools but it might be an explanation as to how these SV annotations made it into Gnomad. https://bioconductor.org/packages/devel/bioc/vignettes/S ...
written 4 months ago by Garan580
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Answer: A: Gold standard CNV Calls for NA12878
... Have you tried some of the Genome In A Bottle resources? [https://jimb.stanford.edu/giab-resources][1] **EDIT** Recent paper by the GIAB group https://www.biorxiv.org/content/10.1101/664623v1 Mt. Sinai School of Medicine has uploaded ~44x PacBio data for NA12878, including raw reads, error-correc ...
written 6 months ago by Garan580
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Comment: C: How can I do in GTAK downstream analysis?
... I guess if you're looking for somatic mutations not germline variants then this complicates things, without non-tumor samples to compare to. I guess you'd also want to take into account the source and age profile of the Gnomad/Exac variant information since I believe some of datasets were recruited ...
written 6 months ago by Garan580
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Answer: A: How can I do in GTAK downstream analysis?
... I take it this is a mendelian rare disease that you are looking for a causal variant? Are the 20 samples trios (parents-proband) or singletons (unrelated cases with similar symptoms), as this will change the filtering strategy? Do you have family history? Population details / Phenotype details? If ...
written 7 months ago by Garan580
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Answer: A: gnomAD: query utilitites
... The Cellbase Swagger restful API might have what you're after, although I'm not sure how many requests it will take if you're looking to bulk query. [http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/][1] [http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/variation/rs11658 ...
written 7 months ago by Garan580
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Comment: C: Storing Varaint data from VCF
... Just to add to the edit I made to the answer: The processing of the VCFs doesn't have to be straight away, you could set up a scheduler to process the files later, and probably just as important to re-annotate the variants on an ongoing basis (keeping the original version). ...
written 8 months ago by Garan580
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Answer: A: Storing Varaint data from VCF
... I developed something similar a long time ago and you're welcome to have a look [https://github.com/pasted/clinical_variant_database][1] It can probably be improved alot. Things to note: - Variants can be of any size so you probably need a start / stop field for the genomic coordinates - The coo ...
written 8 months ago by Garan580
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Answer: A: Anyone know of a useful pedigree drawing program?
... You could try OmicsTools website for some ideas (many are commercial though) [https://omictools.com/pedigree-drawing-category][1], or the University of Alabama at Birmingham's site [https://www.soph.uab.edu/ssg/linkage/pedigreedrawing][2] For suggestions from previously used software i'd go with s ...
written 10 months ago by Garan580

Latest awards to Garan

Scholar 14 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Supporter 14 months ago, voted at least 25 times.
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Recommendations for CNV calling algorithms/programs to benchmark
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 21 months ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 3.7 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 5.0 years ago, created an answer that has been accepted. For A: about the previous version of GATK
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Copy number variation detection tools within exome sequencing
Scholar 5.2 years ago, created an answer that has been accepted. For A: about the previous version of GATK

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